Novel Plant Cells, Plants, and Seeds

ABSTRACT

Disclosed herein are compositions and methods for effecting alterations at a defined location in the genome of a non-epidermal plant cell. Further disclosed are methods for providing plants having a modified phenotype or a modified genome.

PRIORITY CLAIMS AND RELATED APPLICATIONS

This application claims the benefit of priority to U.S. ProvisionalPatent Applications 62/418,078, filed on 4 Nov. 2016, and 62/442,601,filed on 5 Jan. 2017, which are incorporated by reference in theirentirety herein.

INCORPORATION OF SEQUENCE LISTING

The sequence listings contained in the files named “10001P1_ST25.txt”(which is 98 kilobytes measured in operating system Windows 7 x64,created on 4 Nov. 2016 and electronically filed via EFS-Web on 4 Nov.2016) and “98062-02_ST25.txt” (which is ˜100 kilobytes measured inoperating system Windows 8.1 x64, created on 4 Jan. 2017 andelectronically filed via EFS-Web on 5 Jan. 2017), are incorporatedherein by reference in their entirety. The sequence listing contained inthe file named “10001WO1_ST25.txt”, which is 176 kilobytes measured inoperating system Windows 7 x64, created on 3 Nov. 2017, iselectronically filed herewith via EFS-Web and incorporated herein byreference in its entirety.

FIELD

Aspects of this invention relate to agricultural biotechnology.Disclosed herein are novel plant cells, plants and seeds derived fromsuch plant cells and having enhanced traits, and methods of making andusing such plant cells and derived plants and seeds.

BACKGROUND

Recent advances in genome editing technologies have providedopportunities for precise modification of the genome in many types oforganisms, including plants and animals. For example, technologies basedon genome editing proteins, such as zinc finger nucleases, TALENs, andCRISPR systems are advancing rapidly and it is now possible to targetgenetic changes to specific DNA sequences in the genome.

CRISPR technology for editing the genes of eukaryotes is disclosed in USPatent Application Publications 2016/0138008A1 and US2015/0344912A1, andin U.S. Pat. Nos. 8,697,359, 8,771,945, 8,945,839, 8,999,641, 8,993,233,8,895,308, 8,865,406, 8,889,418, 8,871,445, 8,889,356, 8,932,814,8,795,965, and 8,906,616. Cpf1 endonuclease and corresponding guide RNAsand PAM sites are disclosed in US Patent Application Publication2016/0208243 A1. Other CRISPR nucleases useful for editing genomesinclude C2c1 and C2c3 (see Shmakov et al. (2015) Mol. Cell, 60:385-397)and CasX and CasY (see Burstein et al. (2016) Nature,doi:10.1038/nature21059). Plant RNA promoters for expressing CRISPRguide RNA and plant codon-optimized CRISPR Cas9 endonuclease aredisclosed in International Patent Application PCT/US2015/018104(published as WO 2015/131101 and claiming priority to US ProvisionalPatent Application 61/945,700). Methods of using CRISPR technology forgenome editing in plants are disclosed in in US Patent ApplicationPublications US 2015/0082478A1 and US 2015/0059010A1 and inInternational Patent Application PCT/US2015/038767 A1 (published as WO2016/007347 and claiming priority to U.S. Provisional Patent Application62/023,246).

SUMMARY

Disclosed herein are methods for providing novel plant cells, plants,and seeds having one or more altered genetic sequences.

In one aspect, the invention provides a method of delivering a guide RNA(gRNA) (or other sequence-editing guide nucleic acid capable ofdirecting a nuclease to a specific target sequence) to a non-epidermalplant cell in a plant or part of a plant. The gRNA can be provided as aCRISPR RNA (crRNA) or as a single guide RNA (sgRNA) or as apolynucleotide that encodes or is processed to a crRNA or sgRNA, whereinthe gRNA has a nucleotide sequence designed to alter a target nucleotidesequence in the non-epidermal plant cell. In embodiments, thenon-epidermal cell is a cell capable of division and differentiation,such as a meristem cell or a cell in a plant embryo or seed or seedling.In embodiments, the non-epidermal plant cell is in a monocot plant or ina dicot plant, and can be haploid or diploid. In embodiments, thenon-epidermal plant cell contains a nuclease, such as a Cas9 nuclease orother RNA-guided nuclease, that is capable of altering the targetnucleotide sequence; in other embodiments the nuclease is provided tothe non-epidermal plant cell, either together with the crRNA (or othergenome-editing polynucleotide) or separately. The nuclease can beprovided as a functional enzyme (e. g., as a ribonucleoprotein ormicelle or other molecular or supramolecular complex), or as apolynucleotide that encodes the functional nuclease. The targetnucleotide sequence is one or more nucleotide sequences, includingprotein-coding sequence or non-coding sequence or a combination thereof.Embodiments include a plant nuclear sequence, a plant plastid sequence,a plant mitochondrial sequence, a sequence of a symbiont, pest, orpathogen of a plant, and combinations thereof. The crRNA (or othersequence-editing polynucleotide) and the RNA-guided nuclease areprovided separately (e. g., in discrete compositions or in discretesteps), or alternatively are provided simultaneously (e. g., combined ina single composition, or in a single step or treatment). Embodiments ofthe method include one or more delivery steps or treatments, includingtreatment with at least one chemical, enzymatic, or physical agent oruse of techniques such as application of heat or cold, ultrasonication,centrifugation, and electroporation, whereby the gRNA is delivered tothe non-epidermal plant cell. In embodiments, the method furtherincludes growing or regeneration of a seedling, plantlet, or plant fromthe non-epidermal plant cell having the altered target nucleotidesequence. Related aspects include: the non-epidermal plant cell with thealtered target nucleotide sequence provided by the method; pluralities,arrays, and heterogeneous populations of such non-epidermal plant cells;and callus, seedlings, plantlets, and plants and their seeds, grown orregenerated from the non-epidermal plant cell and having the alteredtarget nucleotide sequence, and pluralities, arrays, and heterogeneouspopulations thereof.

In another aspect, the invention provides a method of providing a planthaving a genetic alteration, including the step of delivering aneffector molecule such as a sequence-specific nuclease or a guidenucleic acid to a plant cell capable of division and differentiation,resulting in a genetic alteration of the plant cell, and growing orregenerating a plant from the resulting genetically altered plant cell,wherein the plant includes differentiated cells or tissues having thegenetic alteration. In embodiments, the plant cell is in a plant or partof a plant, is monocot or dicot, is haploid or diploid, and is capableof division and differentiation or capable of growth or regenerationinto callus, a seedling, a plantlet, or a plant. Embodiments includethose wherein the effector molecule is at least one selected from thegroup consisting of: a polynucleotide, a ribonucleoprotein, apolypeptide (for example, a protein, an enzyme, or a nuclease), and apolynucleotide encoding a polypeptide; or a combination thereof.Embodiments of the method include one or more delivery steps ortreatments, including treatment with chemical or physical agents or useof techniques such as application of heat or cold, ultrasonication,centrifugation, and electroporation. Related aspects include plantshaving a genetic alteration provided by the method, heterogeneouspopulations or libraries of such plants, succeeding generations or seedsof such plants, parts of the plants, or products made from the plants ortheir seeds.

In another aspect, the invention provides a method of identifying anucleotide sequence (or alteration of a nucleotide sequence) associatedwith a phenotype of interest, including altering the genome of apopulation of plant cells or protoplasts, optionally growing orregenerating a population of calli, seedlings, plantlets, or plants fromthe population of plant cells or protoplasts, and selecting the plantcells or protoplasts (or calli, seedlings, plantlets, or plants)exhibiting the phenotype of interest. Embodiments of the method includeculturing or growing the plant cells or protoplasts (or calli,seedlings, plantlets, or plants) under conditions that permit expressionof the phenotype of interest.

DETAILED DESCRIPTION OF THE INVENTION

Unless otherwise stated, nucleic acid sequences in the text of thisspecification are given, when read from left to right, in the 5′ to 3′direction. Nucleic acid sequences may be provided as DNA or as RNA, asspecified; disclosure of one necessarily defines the other, as well asnecessarily defines the exact complements, as is known to one ofordinary skill in the art. Where a term is provided in the singular, theinventors also contemplate aspects of the invention described by theplural of that term.

By “polynucleotide” is meant a nucleic acid molecule containing multiplenucleotides and refers to “oligonucleotides” (defined here as apolynucleotide molecule of between 2-25 nucleotides in length) andpolynucleotides of 26 or more nucleotides. Polynucleotides are generallydescribed as single- or double-stranded. Where a polynucleotide containsdouble-stranded regions formed by intra- or intermolecularhybridization, the length of each double-stranded region is convenientlydescribed in terms of the number of base pairs. Aspects of thisinvention include the use of polynucleotides or compositions containingpolynucleotides; embodiments include one or more oligonucleotides orpolynucleotides or a mixture of both, including single- ordouble-stranded RNA or single- or double-stranded DNA or double-strandedDNA/RNA hybrids or chemically modified analogues or a mixture thereof.In various embodiments, the polynucleotide includes a combination ofribonucleotides and deoxyribonucleotides (e. g., syntheticpolynucleotides consisting mainly of ribonucleotides but with one ormore terminal deoxyribonucleotides or synthetic polynucleotidesconsisting mainly of deoxyribonucleotides but with one or more terminaldideoxyribonucleotides), or includes non-canonical nucleotides such asinosine, thiouridine, or pseudouridine. In embodiments, thepolynucleotide includes chemically modified nucleotides (see, e. g.,Verma and Eckstein (1998) Annu. Rev. Biochem., 67:99-134); for example,the naturally occurring phosphodiester backbone of an oligonucleotide orpolynucleotide can be partially or completely modified withphosphorothioate, phosphorodithioate, or methylphosphonateinternucleotide linkage modifications, modified nucleoside bases ormodified sugars can be used in oligonucleotide or polynucleotidesynthesis, and oligonucleotides or polynucleotides can be labelled witha fluorescent moiety (e. g., fluorescein or rhodamine) or other label(e. g., biotin). Modified nucleic acids, particularly modified RNAs, aredisclosed in U.S. Pat. No. 9,464,124, incorporated by reference in itsentirety herein.

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas(CRISPR-associated) systems, or CRISPR systems, are adaptive defensesystems originally discovered in bacteria and archaea. CRISPR systemsuse RNA-guided nucleases termed CRISPR-associated or “Cas” endonucleases(e. g., Cas9 or Cpf1) to cleave foreign DNA. In a typical CRISPR/Cassystem, a Cas endonuclease is directed to a target nucleotide sequence(e. g., a site in the genome that is to be sequence-edited) bysequence-specific, non-coding “guide RNAs” that target single- ordouble-stranded DNA sequences. In microbial hosts, CRISPR loci encodeboth Cas endonucleases and “CRISPR arrays” of the non-coding RNAelements that determine the specificity of the CRISPR-mediated nucleicacid cleavage.

Three classes (I-III) of CRISPR systems have been identified across awide range of bacterial hosts. The well characterized class II CRISPRsystems use a single Cas endonuclease (rather than multiple Casproteins). One class II CRISPR system includes a type II Casendonuclease such as Cas9, a CRISPR RNA (“crRNA”), and atrans-activating crRNA (“tracrRNA”). The crRNA contains a “guide RNA”,typically a 20-nucleotide RNA sequence that corresponds to (i. e., isidentical or nearly identical to, or alternatively is complementary ornearly complementary to) a 20-nucleotide target DNA sequence. The crRNAalso contains a region that binds to the tracrRNA to form a partiallydouble-stranded structure which is cleaved by RNase III, resulting in acrRNA/tracrRNA hybrid. The crRNA/tracrRNA hybrid then directs the Cas9endonuclease to recognize and cleave the target DNA sequence.

The target DNA sequence must generally be adjacent to a “protospaceradjacent motif” (“PAM”) that is specific for a given Cas endonuclease;however, PAM sequences are short and relatively non-specific, appearingthroughout a given genome. CRISPR endonucleases identified from variousprokaryotic species have unique PAM sequence requirements; examples ofPAM sequences include 5′-NGG (Streptococcus pyogenes), 5′-NNAGAA(Streptococcus thermophilus CRISPR1), 5′-NGGNG (Streptococcusthermophilus CRISPR3), and 5′-NNNGATT (Neisseria meningitidis). Someendonucleases, e. g., Cas9 endonucleases, are associated with G-rich PAMsites, e. g., 5′-NGG, and perform blunt-end cleaving of the target DNAat a location 3 nucleotides upstream from (5′ from) the PAM site.

Another class II CRISPR system includes the type V endonuclease Cpf1,which is a smaller endonuclease than is Cas9; examples include AsCpf1(from Acidaminococcus sp.) and LbCpf1 (from Lachnospiraceae sp.).Cpf1-associated CRISPR arrays are processed into mature crRNAs withoutthe requirement of a tracrRNA; in other words, a Cpf1 system requiresonly the Cpf1 nuclease and a crRNA to cleave the target DNA sequence.Cpf1 endonucleases, are associated with T-rich PAM sites, e. g., 5′-TTN.Cpf1 can also recognize a 5′-CTA PAM motif. Cpf1 cleaves the target DNAby introducing an offset or staggered double-strand break with a 4- or5-nucleotide 5′ overhang, for example, cleaving a target DNA with a5-nucleotide offset or staggered cut located 18 nucleotides downstreamfrom (3′ from) from the PAM site on the coding strand and 23 nucleotidesdownstream from the PAM site on the complimentary strand; the5-nucleotide overhang that results from such offset cleavage allows moreprecise genome editing by DNA insertion by homologous recombination thanby insertion at blunt-end cleaved DNA. See, e. g., Zetsche et al. (2015)Cell, 163:759-771. Other CRISPR nucleases useful in methods andcompositions of the invention include C2c1 and C2c3 (see Shmakov et al.(2015) Mol. Cell, 60:385-397) and CasX and CasY (see Burstein et al.(2016) Nature, doi:10.1038/nature21059). Like other CRISPR nucleases,C2c1 from Alicyclobacillus acidoterrestris (AacC2c1) requires a guideRNA and PAM recognition site; C2c1 cleavage results in a staggeredseven-nucleotide DSB in the target DNA (see Yang et al. (2016) Cell,167:1814-1828.e12) and is reported to have high mismatch sensitivity,thus reducing off-target effects (see Liu et al. (2016) Mol. Cell,available on line atdx[dot]doi[dot]org/10[dot]1016/j[dot]molcel[dot]2016[dot]11.040). Yetother CRISPR nucleases include nucleases identified from the genomes ofuncultivated microbes, such as CasX and CasY; see Burstein et al. (2016)Nature, doi:10.1038/nature21059.

For the purposes of gene editing, CRISPR arrays can be designed tocontain one or multiple guide RNA sequences corresponding to a desiredtarget DNA sequence; see, for example, Cong et al. (2013) Science,339:819-823; Ran et al. (2013) Nature Protocols, 8:2281-2308. At least16 or 17 nucleotides of gRNA sequence are required by Cas9 for DNAcleavage to occur; for Cpf1 at least 16 nucleotides of gRNA sequence areneeded to achieve detectable DNA cleavage and at least 18 nucleotides ofgRNA sequence were reported necessary for efficient DNA cleavage invitro; see Zetsche et al. (2015) Cell, 163:759-771. In practice, guideRNA sequences are generally designed to have a length of between 17-24nucleotides (frequently 19, 20, or 21 nucleotides) and exactcomplementarity (i. e., perfect base-pairing) to the targeted gene ornucleic acid sequence; guide RNAs having less than 100% complementarityto the target sequence can be used (e. g., a gRNA with a length of 20nucleotides and between 1-4 mismatches to the target sequence) but canincrease the potential for off-target effects. The design of effectiveguide RNAs for use in plant genome editing is disclosed in US PatentApplication Publication 2015/0082478 A1, the entire specification ofwhich is incorporated herein by reference. More recently, efficient geneediting has been achieved using a chimeric “single guide RNA” (“sgRNA”),an engineered (synthetic) single RNA molecule that mimics a naturallyoccurring crRNA-tracrRNA complex and contains both a tracrRNA (forbinding the nuclease) and at least one crRNA (to guide the nuclease tothe sequence targeted for editing); see, for example, Cong et al. (2013)Science, 339:819-823; Xing et al. (2014) BMC Plant Biol., 14:327-340.Chemically modified sgRNAs have been demonstrated to be effective ingenome editing; see, for example, Hendel et al. (2015) NatureBiotechnol., 985-991.

CRISPR-type genome editing has value in various aspects of agricultureresearch and development. CRISPR elements, i. e., CRISPR endonucleasesand CRISPR single-guide RNAs, are useful in effecting genome editingwithout remnants of the CRISPR elements or selective genetic markersoccurring in progeny. Alternatively, genome-inserted CRISPR elements areuseful in plant lines adapted for multiplex genetic screening andbreeding. For instance, a plant species can be created to express one ormore of a CRISPR endonuclease such as a Cas9- or a Cpf1-typeendonuclease or combinations with unique PAM recognition sites. Cpf1endonuclease and corresponding guide RNAs and PAM sites are disclosed inUS Patent Application Publication 2016/0208243 A1, which is incorporatedherein by reference for its disclosure of DNA encoding Cpf1endonucleases and guide RNAs and PAM sites. Introduction of one or moreof a wide variety of CRISPR guide RNAs that interact with CRISPRendonucleases integrated into a plant genome or otherwise provided to aplant is useful for genetic editing for providing desired phenotypes ortraits, for trait screening, or for trait introgression. Multipleendonucleases can be provided in expression cassettes with theappropriate promoters to allow multiple genome editing in a spatially ortemporally separated fashion in either in chromosome DNA or episome DNA.

Whereas wild-type Cas9 generates double-strand breaks (DSBs) at specificDNA sequences targeted by a gRNA, a number of CRISPR endonucleaseshaving modified functionalities are available, for example: (1) a“nickase” version of Cas9 generates only a single-strand break; (2) acatalytically inactive Cas9 (“dCas9”) does not cut the target DNA butinterferes with transcription; dCas9 can further be fused with arepressor peptide; (3) a catalytically inactive Cas9 (“dCas9”) fused toan activator peptide can activate or increase gene expression; (4) acatalytically inactive Cas9 (dCas9) fused to FokI nuclease(“dCas9-FokI”) can be used to generate DSBs at target sequenceshomologous to two gRNAs. See, e. g., the numerous CRISPR/Cas9 plasmidsdisclosed in and publicly available from the Addgene repository(Addgene, 75 Sidney St., Suite 550A, Cambridge, Mass. 02139;addgene[dot]org/crispr/). A “double nickase” Cas9 that introduces twoseparate double-strand breaks, each directed by a separate guide RNA, isdescribed as achieving more accurate genome editing by Ran et al. (2013)Cell, 154:1380-1389.

CRISPR technology for editing the genes of eukaryotes is disclosed in USPatent Application Publications 2016/0138008A1 and US2015/0344912A1, andin U.S. Pat. Nos. 8,697,359, 8,771,945, 8,945,839, 8,999,641, 8,993,233,8,895,308, 8,865,406, 8,889,418, 8,871,445, 8,889,356, 8,932,814,8,795,965, and 8,906,616. Cpf1 endonuclease and corresponding guide RNAsand PAM sites are disclosed in US Patent Application Publication2016/0208243 A1. Plant RNA promoters for expressing CRISPR guide RNA andplant codon-optimized CRISPR Cas9 endonuclease are disclosed inInternational Patent Application PCT/US2015/018104 (published as WO2015/131101 and claiming priority to US Provisional Patent Application61/945,700). Methods of using CRISPR technology for genome editing inplants are disclosed in in US Patent Application Publications US2015/0082478A1 and US 2015/0059010A1 and in International PatentApplication PCT/US2015/038767 A1 (published as WO 2016/007347 andclaiming priority to U.S. Provisional Patent Application 62/023,246).All of the patent publications referenced in this paragraph areincorporated herein by reference in their entirety.

In some embodiments, one or more vectors driving expression of one ormore polynucleotides encoding elements of a genome-editing system (e.g., encoding a guide RNA or a nuclease) are introduced into a plantcell, whereby these elements, when expressed, result in alteration of atarget nucleotide sequence. In embodiments, a vector includes aregulatory element such as a promoter operably linked to one or morepolynucleotides encoding elements of a genome-editing system. In suchembodiments, expression of these polynucleotides can be controlled byselection of the appropriate promoter, particularly promoters functionalin a plant cell; useful promoters include constitutive, conditional,inducible, and temporally or spatially specific promoters (e. g., atissue specific promoter, a developmentally regulated promoter, or acell cycle regulated promoter). In embodiments the promoter is operablylinked to nucleotide sequences encoding multiple guide RNAs, wherein thesequences encoding guide RNAs are separated by a cleavage site such as anucleotide sequence encoding a microRNA recognition/cleavage site or aself-cleaving ribozyme (see, e. g., Ferré-D'Amaré and Scott (2014) ColdSpring Harbor Perspectives Biol., 2:a003574). In embodiments, thepromoter is a pol II promoter operably linked to a nucleotide sequenceencoding one or more guide RNAs. In embodiments, the promoter operablylinked to one or more polynucleotides encoding elements of agenome-editing system is a constitutive promoter that drives DNAexpression in plant cells including in the nucleus or in an organellesuch as a chloroplast or mitochondrion. Examples of constitutivepromoters include a CaMV 35S promoter as disclosed in U.S. Pat. Nos.5,858,742 and 5,322,938, a rice actin promoter as disclosed in U.S. Pat.No. 5,641,876, a maize chloroplast aldolase promoter as disclosed inU.S. Pat. No. 7,151,204, and a opaline synthase (NOS) and octapinesynthase (OCS) promoter from Agrobacterium tumefaciens. In embodiments,the promoter operably linked to one or more polynucleotides encodingelements of a genome-editing system is a promoter from figwort mosaicvirus (FMV), a RUBISCO promoter, or a pyruvate phosphate dikinase (PDK)promoter, which is active in the chloroplasts of mesophyll cells. Othercontemplated promoters include cell-specific or tissue-specific ordevelopmentally regulated promoters, for example, a promoter that limitsthe expression of the nucleic acid targeting system to germline orreproductive cells (e. g., promoters of genes encoding DNA ligases,recombinases, replicases, or other genes specifically expressed ingermline or reproductive cells); in such embodiments, thenuclease-mediated genetic modification (e. g., chromosomal or episomaldouble-stranded DNA cleavage) is limited only those cells from which DNAis inherited in subsequent generations, which is advantageous where itis desirable that expression of the genome-editing system be limited inorder to avoid genotoxicity or other unwanted effects. All of the patentpublications referenced in this paragraph are incorporated herein byreference in their entirety.

In some embodiments, elements of a genome-editing system (e. g., anRNA-guided nuclease and a guide RNA) are operably linked to separateregulatory elements on separate vectors. In other embodiments, two ormore elements of a genome-editing system expressed from the same ordifferent regulatory elements or promoters are combined in a singlevector, optionally with one or more additional vectors providing anyadditional necessary elements of a genome-editing system not included inthe first vector. For example, multiple guide RNAs can be expressed fromone vector, with the appropriate RNA-guided nuclease expressed from asecond vector. In another example, one or more vectors for theexpression of one or more guide RNAs (e. g., crRNAs or sgRNAs) aredelivered to a plant cell that expresses the appropriate RNA-guidednuclease, or to a plant cell that otherwise contains the nuclease, suchas by way of prior administration thereto of a vector for in vivoexpression of the nuclease.

Genome-editing system elements that are combined in a single vector maybe arranged in any suitable orientation, such as one element located 5′with respect to (“upstream” of) or 3′ with respect to (“downstream” of)a second element. The coding sequence of one element may be located onthe same or opposite strand of the coding sequence of a second element,and oriented in the same or opposite direction. In embodiments, theendonuclease and the nucleic acid-targeting guide RNA may be operablylinked to and expressed from the same promoter. In embodiments, a singlepromoter drives expression of a transcript encoding an endonuclease andthe guide RNA, embedded within one or more intron sequences (e. g., eachin a different intron, two or more in at least one intron, or all in asingle intron), which can be plant-derived; such use of introns isespecially contemplated when the expression vector is being transformedor transfected into a monocot cell.

Expression vectors provided herein may contain a DNA segment near the 3′end of an expression cassette that acts as a signal to terminatetranscription and directs polyadenylation of the resultant mRNA. Theseare commonly referred to as “3′-untranslated regions” or “3′-UTRs” or“polyadenylation signals”. Useful 3′ elements include: Agrobacteriumtumefaciens nos 3′, tml 3′, tmr 3′, tms 3′, ocs 3′, and tr7 3′ elementsdisclosed in U.S. Pat. No. 6,090,627, incorporated herein by reference,and 3′ elements from plant genes such as the heat shock protein 17,ubiquitin, and fructose-1,6-biphosphatase genes from wheat (Triticumaestivum), and the glutelin, lactate dehydrogenase, and beta-tubulingenes from rice (Oryza sativa), disclosed in US Patent ApplicationPublication 2002/0192813 A1, incorporated herein by reference.

In certain embodiments, a vector or an expression cassette includesadditional components, e. g., a polynucleotide encoding a drugresistance or herbicide gene or a polynucleotide encoding a detectablemarker such as green fluorescent protein (GFP) or beta-glucuronidase(gus) to allow convenient screening or selection of cells expressing thevector. In embodiments, the vector or expression cassette includesadditional elements for improving delivery to the plant cell or fordirecting or modifying expression of one or more genome-editing systemelements, for example, fusing a sequence encoding a cell-penetratingpeptide, localization signal, transit, or targeting peptide to theRNA-guided nuclease, or adding a nucleotide sequence to stabilize aguide RNA; such fusion proteins (and the polypeptides encoding suchfusion proteins) or combination polypeptides, as well as expressioncassettes and vectors for their expression in a cell, are specificallyclaimed. In embodiments, an RNA-guided nuclease (e. g., Cas9, Cpf1,CasY, CasX, C2c1, or C2c3) is fused to a localization signal, transit,or targeting peptide, e. g., a nuclear localization signal (NLS), achloroplast transit peptide (CTP), or a mitochondrial targeting peptide(MTP); in a vector or an expression cassette, the nucleotide sequenceencoding any of these can be located either 5′ and/or 3′ to the DNAencoding the nuclease. For example, a plant-codon-optimized Cas9(pco-Cas9) from Streptococcus pyogenes and S. thermophilus containingnuclear localization signals and codon-optimized for expression in maizeis disclosed in PCT/US2015/018104 (published as WO/2015/131101 andclaiming priority to U.S. Provisional Patent Application 61/945,700),incorporated herein by reference. In another example, achloroplast-targeting RNA is appended to the 5′ end of an mRNA encodingan endonuclease to drive the accumulation of the mRNA in chloroplasts;see Gomez, et al. (2010) Plant Signal Behav., 5: 1517 1519. In anembodiment, a Cas9 from Streptococcus pyogenes is fused to a nuclearlocalization signal (NLS), such as the NLS from SV40. In an embodiment,a Cas9 from Streptococcus pyogenes is fused to a cell-penetratingpeptide (CPP), such as octa-arginine or nona-arginine or a homoarginine12-mer oligopeptide, or a CPP disclosed in the database ofcell-penetrating peptides CPPsite 2.0, publicly available atcrdd[dot]osdd[dot]net/raghava/cppsite/. In an embodiment, a Cas9 fromStreptococcus pyogenes is fused to a chloroplast transit peptide (CTP)sequence. In embodiments, a CTP sequence is obtained from any nucleargene that encodes a protein that targets a chloroplast, and the isolatedor synthesized CTP DNA is appended to the 5′ end of the DNA that encodesa nuclease targeted for use in a chloroplast. Chloroplast transitpeptides and their use are described in U.S. Pat. Nos. 5,188,642,5,728,925, and 8,420,888, all of which are incorporated herein byreference in their entirety. Specifically, the CTP nucleotide sequencesprovided with the sequence identifier (SEQ ID) numbers 12-15 and 17-22of U.S. Pat. No. 8,420,888 are incorporated herein by reference. In anembodiment, a Cas9 from Streptococcus pyogenes is fused to amitochondrial targeting peptide (MTP), such as a plant MTP sequence;see, e. g., Jores et al. (2016) Nature Communications, 7:12036-12051.

Plasmids designed for use in plants and encoding CRISPR genome editingelements (CRISPR nucleases and guide RNAs) are publicly available fromplasmid repositories such as Addgene (Cambridge, Mass.; also see“addgene[dot]com”). In embodiments, such plasmids are used to co-expressboth CRISPR nuclease mRNA and guide RNA(s); in other embodiments, CRISPRendonuclease mRNA and guide RNA are delivered from separate plasmids. Inembodiments, the plasmids are Agrobacterium TI plasmids. Materials andmethods for preparing expression cassettes and vectors for CRISPRendonuclease and guide RNA for stably integrated and/or transient planttransformation are disclosed in PCT/US2015/018104 (published asWO/2015/131101 and claiming priority to U.S. Provisional PatentApplication 61/945,700), US Patent Application Publication 2015/0082478A1, and PCT/US2015/038767 (published as WO/2016/007347 and claimingpriority to U.S. Provisional Patent Application 62/023,246), all ofwhich are incorporated herein by reference in their entirety. Inembodiments, such expression cassettes are isolated linear fragments, orare part of a larger construct that includes bacterial replicationelements and selectable markers; such embodiments are useful, e. g., forparticle bombardment or nanoparticle delivery or protoplasttransformation. In embodiments, the expression cassette is adjacent toor located between T-DNA borders or contained within a binary vector, e.g., for Agrobacterium-mediated transformation. In embodiments, a plasmidencoding a CRISPR nuclease is delivered to a plant cell for stableintegration of the CRISPR nuclease into the plant cell's genome, oralternatively for transient expression of the CRISPR nuclease. Inembodiments, plasmids encoding a CRISPR nuclease are delivered to aplant cell to achieve stable or transient expression of the CRISPRnuclease, and one or multiple guide RNAs (such as a library ofindividual guide RNAs or multiple pooled guide RNAs) or plasmidsencoding the guide RNAs are delivered to the plant cell individually orin combinations, thus providing libraries or arrays of plant cells,plant parts or tissues, embryos, seeds, or intact plants, in which avariety of genome edits are provided by the different guide RNAs.

In certain embodiments where the genome-editing system is a CRISPRsystem, expression of the guide RNA is driven by a plant U6 spliceosomalRNA promoter, which can be native to the plant being edited or from adifferent plant, e. g., a U6 promoter from maize, tomato, or soybeansuch as those disclosed in PCT/US2015/018104 (published as WO2015/131101 and claiming priority to U.S. Provisional Patent Application61/945,700), incorporated herein by reference, or a homologue thereof;such a promoter is operably linked to DNA encoding the guide RNA fordirecting an endonuclease, followed by a suitable 3′ element such as aU6 poly-T terminator. In another embodiment, an expression cassette forexpressing guide RNAs in plants is used, wherein the promoter is a plantU3, 7SL (signal recognition particle RNA), U2, or U5 promoter, orchimerics thereof, e. g., as described in PCT/US2015/018104 (publishedas WO 2015/131101 and claiming priority to U.S. Provisional PatentApplication 61/945,700), incorporated herein by reference. When multipleor different guide RNA sequences are used, a single expression constructmay be used to correspondingly direct the genome editing activity to themultiple or different target sequences in a cell. In variousembodiments, a single vector includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,about 15, about 20, or more guide RNA sequences; in other embodiments,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, about 15, about 20, or more guide RNAsequences are provided on multiple vectors, which can be delivered toone or multiple cells (e. g., delivered to an array of plant cells,plant parts or tissues, embryos, seeds, or plants).

In embodiments, one or more guide RNAs and the corresponding RNA-guidednuclease are delivered together or simultaneously. In other embodiments,one or more guide RNAs and the corresponding RNA-guided nuclease aredelivered separately; these can be delivered in separate, discrete stepsand using the same or different delivery techniques. In an example, anRNA-guided nuclease is delivered to a plant cell by particlebombardment, on carbon nanotubes, or by Agrobacterium-mediatedtransformation, and one or more guide RNAs is delivered to the plantcell in a separate step using the same or different delivery technique.In embodiments, an RNA-guided nuclease encoded by a DNA molecule or anmRNA is delivered to a plant cell with enough time prior to delivery ofthe guide RNA to permit expression of the nuclease in the plant cell;for example, an RNA-guided nuclease encoded by a DNA molecule or an mRNAis delivered to a plant cell between 1-12 hours (e. g., about 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, or 12 hours, or between about 1-6 hours orbetween about 2-6 hours) prior to the delivery of the guide RNA to theplant cell. In embodiments, whether the RNA-guided nuclease is deliveredsimultaneously with or separately from an initial dose of guide RNA,succeeding “booster” doses of guide RNA are delivered subsequent to thedelivery of the initial dose; for example, a second “booster” dose ofguide RNA is delivered to a plant cell between 1-12 hours (e. g., about1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 hours, or between about 1-6hours or between about 2-6 hours) subsequent to the delivery of theinitial dose of guide RNA to the plant cell. Similarly, in someembodiments, multiple deliveries of an RNA-guided nuclease or of a DNAmolecule or an mRNA encoding an RNA-guided nuclease are used to increaseefficiency of the genome modification.

In embodiments, the desired genome modification involves homologousrecombination, wherein one or more double-stranded DNA break in thetarget nucleotide sequence is generated by the RNA-guided nuclease andguide RNA(s), followed by repair of the break(s) using a homologousrecombination mechanism (“homology-directed repair”). In suchembodiments, a donor template that encodes the desired nucleotidesequence to be inserted or knocked-in at the double-stranded break isprovided to the cell; examples of suitable templates includesingle-stranded DNA templates and double-stranded DNA templates (e. g.,in the form of a plasmid). In general, a donor template encoding anucleotide change over a region of less than about 50 nucleotides isconveniently provided in the form of single-stranded DNA; larger donortemplates (e. g., more than 100 nucleotides) are often convenientlyprovided as double-stranded DNA plasmids. In embodiments, the variouscompositions and methods described herein for delivering guide RNAs andnucleases are also generally useful for delivering the donor templatepolynucleotide to the plant cell; this delivery can be simultaneouswith, or separate from (generally after) delivery of the nuclease andguide RNA to the cell. For example, a donor template can be transientlyintroduced into a plant cell, optionally with the nuclease and/or gRNA;in embodiments, the donor template is provided to the cell in a quantitythat is sufficient to achieve the desired homology-directed repair butthat does not persist in the cell after a given period of time (e. g.,after one or more cell division cycles). In embodiments, a donortemplate has a core nucleotide sequence that differs from the targetnucleotide sequence (e. g., a homologous endogenous genomic region) byat least 1, at least 5, at least 10, at least 20, at least 30, at least40, at least 50, or more nucleotides. This core sequence is flanked by“homology arms” or regions of high sequence identity with the targetednucleotide sequence; in embodiments, the regions of high identityinclude at least 10, at least 50, at least 100, at least 150, at least200, at least 300, at least 400, at least 500, at least 600, at least750, or at least 1000 nucleotides on each side of the core sequence. Inembodiments where the donor template is in the form of a single-strandedDNA, the core sequence is flanked by homology arms including at least10, at least 20, at least 30, at least 40, at least 50, at least 60, atleast 70, at least 80, or at least 100 nucleotides on each side of thecore sequence. In embodiments where the donor template is in the form ofa double-stranded DNA plasmid, the core sequence is flanked by homologyarms including at least 500, at least 600, at least 700, at least 800,at least 900, or at least 1000 nucleotides on each side of the coresequence. In an embodiment, two separate double-strand breaks areintroduced into the cell's target nucleotide sequence with a “doublenickase” Cas9 (see Ran et al. (2013) Cell, 154:1380-1389), followed bydelivery of the donor template.

Methods of Altering a Target Nucleotide Sequence in a Plant Cell

In one aspect the invention provides a method of delivering a guide RNA(gRNA) to a plant cell, particularly a non-epidermal plant cell, whereinthe non-epidermal plant cell is in a plant or part of a plant, whereinthe gRNA has a nucleotide sequence designed to alter a target nucleotidesequence in the non-epidermal plant cell, wherein the gRNA is providedas a polynucleotide composition including: (i) a CRISPR RNA (crRNA) thatincludes the gRNA, or a polynucleotide that encodes a crRNA, or apolynucleotide that is processed into a crRNA; or (ii) a single guideRNA (sgRNA) that includes the gRNA, or a polynucleotide that encodes ansgRNA, or a polynucleotide that is processed into an sgRNA; wherein thedelivery of the polynucleotide composition includes at least onetreatment selected from the group consisting of: direct application;soaking or imbibition; vacuum infiltration; application of negative orpositive pressure; introduction into the vascular system;microinjection; application of ultrasound or vibration; application ofhydrodynamic pressure, friction, cavitation or shear stress; vortexing;centrifugation; mechanical cell wall or cell membrane deformation orbreakage; enzymatic cell wall or cell membrane breakage orpermeabilization; abrasion; electroporation; and treatment with at leastone chemical, enzymatic, or physical agent; whereby the gRNA isdelivered to the non-epidermal plant cell. In embodiments, delivery ofthe gRNA results in alteration of the target nucleotide sequence in thenon-epidermal plant cell.

The target nucleotide sequence is one or more nucleotide sequences,including protein-coding sequence or non-coding sequence or acombination thereof. Embodiments include a plant nuclear sequence, aplant plastid sequence, a plant mitochondrial sequence, a sequence of asymbiont, pest, or pathogen of a plant, and combinations thereof.Embodiments include exons, introns, regulatory sequences includingpromoters, other 5′ elements and 3′ elements, and genomic loci encodingnon-coding RNAs including long non-coding RNAs (lncRNAs), microRNAs(miRNAs), and trans-acting siRNAs (ta-siRNAs). In embodiments, multipletarget nucleotide sequences are altered, for example, by delivery ofmultiple gRNAs to the non-epidermal plant cell; the multiple targetnucleotide sequences can be part of the same gene (e. g., differentlocations in a single coding region or in different exons of aprotein-coding gene) or different genes.

In embodiments, the guide RNA (gRNA) has a sequence of between 16-24nucleotides in length (e. g., 16, 17, 18, 19, 20, 21, 22, 23, or 24nucleotides in length). Specific embodiments include gRNAs of 19, 20, or21 nucleotides in length and having 100% complementarity to the targetnucleotide sequence. In many embodiments the gRNA has exactcomplementarity (i. e., perfect base-pairing) to the target nucleotidesequence; in certain other embodiments the gRNA has less than 100%complementarity to the target nucleotide sequence. The design ofeffective gRNAs for use in plant genome editing is disclosed in USPatent Application Publication 2015/0082478 A1, the entire specificationof which is incorporated herein by reference. Efficient Cas9-mediatedgene editing has been achieved using a chimeric “single guide RNA”(“sgRNA”), an engineered (synthetic) single RNA molecule that mimics anaturally occurring crRNA-tracrRNA complex and contains both a tracrRNA(for binding the nuclease) and at least one crRNA (to guide the nucleaseto the sequence targeted for editing).

Thus, in certain embodiments wherein the nuclease is a Cas9-typenuclease, the gRNA can be provided as a polynucleotide compositionincluding: (a) a CRISPR RNA (crRNA) that includes the gRNA together witha separate tracrRNA, or (b) at least one polynucleotide that encodes acrRNA and a tracrRNA (on a single polynucleotide or on separatepolynucleotides), or (c) at least one polynucleotide that is processedinto one or more crRNAs and a tracrRNA. In other embodiments wherein thenuclease is a Cas9-type nuclease, the gRNA can be provided as apolynucleotide composition including a CRISPR RNA (crRNA) that includesthe gRNA, and the required tracrRNA is provided in a separatecomposition or in a separate step, or is otherwise provided to the plantcell (for example, to a plant cell located in a plant part or tissue,embryo, seed, or plants stably or transiently expressing the tracrRNAfrom a polynucleotide encoding the tracrRNA). In other embodimentswherein the nuclease is a Cas9-type nuclease, the gRNA can be providedas a polynucleotide composition including: (a) a single guide RNA(sgRNA) that includes the gRNA, or (b) a polynucleotide that encodes ansgRNA, or (c) a polynucleotide that is processed into an sgRNA.Cpf1-mediated gene editing does not require a tracrRNA; thus, inembodiments wherein the nuclease is a Cpf1-type nuclease, the gRNA isprovided as a polynucleotide composition including (a) a CRISPR RNA(crRNA) that includes the gRNA, or (b) a polynucleotide that encodes acrRNA, or (c) a polynucleotide that is processed into a crRNA.

In embodiments of the method, the polynucleotide composition optionallyincludes an RNA-guided nuclease, or a polynucleotide that encodes theRNA-guided nuclease. In other embodiments of the method, the methodfurther includes the step of providing to the non-epidermal plant cellan RNA-guided nuclease or a polynucleotide that encodes the RNA-guidednuclease. In other embodiments of the method, the non-epidermal plantcell includes an RNA-guided nuclease or a polynucleotide that encodesthe RNA-guided nuclease; in an example the non-epidermal plant cell isin or from a transgenic plant that expresses the RNA-guided nuclease. Inembodiments, the RNA-guided nuclease is selected from the groupconsisting of an RNA-guided DNA endonuclease, a type II Cas nuclease, aCas9, a type V Cas nuclease, a Cpf1, a CasY, a CasX, a C2c1, a C2c3, anengineered RNA-guided nuclease, and a codon-optimized RNA-guidednuclease. In embodiments, the polynucleotide that encodes the RNA-guidednuclease is, for example, DNA that encodes the RNA-guided nuclease andis stably integrated in the genome of the non-epidermal plant cell, DNAor RNA that encodes the RNA-guided nuclease and is transiently presentin or introduced into the non-epidermal plant cell; such DNA or RNA canbe introduced, e. g., by using a vector such as a plasmid or viralvector or as an mRNA.

In embodiments of the method that further include the step of providingto the non-epidermal plant cell an RNA-guided nuclease or apolynucleotide that encodes the RNA-guided nuclease, the RNA-guidednuclease is provided simultaneously with the polynucleotide compositionthat includes the gRNA, or in a separate step that precedes or followsthe step of providing the polynucleotide composition. In embodiments,the polynucleotide composition that includes the gRNA further includesan RNA-guided nuclease or a polynucleotide that encodes the RNA-guidednuclease. In other embodiments, there is provided a separate compositionthat includes an RNA-guided nuclease or a polynucleotide that encodesthe RNA-guided nuclease. In embodiments, the RNA-guided nuclease isprovided as a ribonucleoprotein (RNP) complex, e. g., a preassembled RNPthat includes the RNA-guided nuclease complexed with a polynucleotideincluding the gRNA or encoding a gRNA, or a preassembled RNP thatincludes a polynucleotide that encodes the RNA-guided nuclease (andoptionally encodes the gRNA, or is provided with a separatepolynucleotide including the gRNA or encoding a gRNA), complexed with aprotein. In embodiments, the RNA-guided nuclease is a fusion protein, i.e., wherein the RNA-guided nuclease is covalently bound through apeptide bond to a cell-penetrating peptide, a nuclear localizationsignal peptide, a chloroplast transit peptide, or a mitochondrialtargeting peptide; such fusion proteins are conveniently encoded in asingle nucleotide sequence, optionally including codons for linkingamino acids. In embodiments, the RNA-guided nuclease or a polynucleotidethat encodes the RNA-guided nuclease is provided as a complex with acell-penetrating peptide or other transfecting agent. In embodiments,the RNA-guided nuclease or a polynucleotide that encodes the RNA-guidednuclease is complexed with, or covalently or non-covalently bound to, afurther element, e. g., a carrier molecule, an antibody, an antigen, aviral movement protein, a polymer, a detectable label (e. g., a moietydetectable by fluorescence, radioactivity, or enzymatic orimmunochemical reaction), a quantum dot, or a particulate ornanoparticulate. In embodiments, the RNA-guided nuclease or apolynucleotide that encodes the RNA-guided nuclease is provided in asolution, or is provided in a liposome, micelle, emulsion, reverseemulsion, suspension, or other mixed-phase composition.

The RNA-guided nuclease is provided to the non-epidermal plant cell byany suitable technique. In embodiments, the RNA-guided nuclease isprovided by directly contacting the non-epidermal plant cell with theRNA-guided nuclease or the polynucleotide that encodes the RNA-guidednuclease. In embodiments, the RNA-guided nuclease is provided bytransporting the RNA-guided nuclease or a polynucleotide that encodesthe RNA-guided nuclease into the non-epidermal plant cell using achemical, enzymatic, or physical agent as provided in detail below inthe paragraphs following the heading “Delivery Agents”. In embodiments,the RNA-guided nuclease is provided by bacterially mediated (e. g.,Agrobacterium sp., Rhizobium sp., Sinorhizobium sp., Mesorhizobium sp.,Bradyrhizobium sp., Azobacter sp., Phyllobacterium sp.) transfection ofthe non-epidermal plant cell with a polynucleotide encoding theRNA-guided nuclease; see, e. g., Broothaerts et al. (2005) Nature,433:629-633. In an embodiment, the RNA-guided nuclease is provided bytranscription in the non-epidermal plant cell of a DNA that encodes theRNA-guided nuclease and is stably integrated in the genome of thenon-epidermal plant cell or that is provided to the non-epidermal plantcell in the form of a plasmid or expression vector (e. g., a viralvector) that encodes the RNA-guided nuclease (and optionally encodes oneor more gRNAs, crRNAs, or sgRNAs, or is optionally provided with aseparate plasmid or vector that encodes one or more gRNAs, crRNAs, orsgRNAs). In embodiments, the RNA-guided nuclease is provided to thenon-epidermal plant cell as a polynucleotide that encodes the RNA-guidednuclease, e. g., in the form of an mRNA encoding the nuclease.

Where a polynucleotide is concerned (e. g., a crRNA that includes thegRNA together with a separate tracrRNA, or at least one polynucleotidethat encodes a crRNA and a tracrRNA (on a single polynucleotide or onseparate polynucleotides), or at least one polynucleotide that isprocessed into one or more crRNAs and a tracrRNA, or an sgRNA thatincludes the gRNA, or a polynucleotide that encodes an sgRNA, or apolynucleotide that is processed into an sgRNA, or a polynucleotide thatencodes the RNA-guided nuclease), embodiments of the polynucleotideinclude: (a) double-stranded RNA; (b) single-stranded RNA; (c)chemically modified RNA; (d) double-stranded DNA; (e) single-strandedDNA; (f) chemically modified DNA; or (g) a combination of (a)-(f). Whereexpression of a polynucleotide is involved (e. g., expression of a crRNAfrom a DNA encoding the crRNA, or expression and translation of aRNA-guided nuclease from a DNA encoding the nuclease), in someembodiments it is sufficient that expression be transient, i. e., notnecessarily permanent or stable in the plant cell. Certain embodimentsof the polynucleotide further include additional nucleotide sequencesthat provide useful functionality; non-limiting examples of suchadditional nucleotide sequences include an aptamer or riboswitchsequence, nucleotide sequence that provides secondary structure such asstem-loops or that provides a sequence-specific site for an enzyme (e.g., a sequence-specific recombinase or endonuclease site), T-DNA (e. g.,DNA sequence encoding a gRNA, crRNA, tracrRNA, or sgRNA is enclosedbetween left and right T-DNA borders from Agrobacterium spp. or fromother bacteria that infect or induce tumours in plants), a DNAnuclear-targeting sequence, a regulatory sequence such as a promotersequence, and a transcript-stabilizing sequence. Certain embodiments ofthe polynucleotide include those wherein the polynucleotide is complexedwith, or covalently or non-covalently bound to, a non-nucleic acidelement, e. g., a carrier molecule, an antibody, an antigen, a viralmovement protein, a cell-penetrating or pore-forming peptide, a polymer,a detectable label, a quantum dot, or a particulate or nanoparticulate.

Generally, the non-epidermal plant cell is not an isolated plant cell(e. g., not a plant cell or protoplast isolated from plant tissue or insuspension or plate culture) and is a cell located in an intact orgrowing plant or in a plant part or tissue. In embodiments, thenon-epidermal plant cell is capable of division and furtherdifferentiation. In embodiments, the non-epidermal plant cell is locatedin a plant or part of a plant selected from the group consisting of aplant tissue, a whole plant, an intact nodal bud, a shoot apex or shootapical meristem, a root apex or root apical meristem, lateral meristem,intercalary meristem, a seedling (e. g., a germinating seed or smallseedling or a larger seedling with one or more true leaves), a wholeseed (e. g., an intact seed, or a seed with part or all of its seed coatremoved or treated to make permeable), a halved seed or other seedfragment, an embryo (e. g., a mature dissected zygotic embryo, adeveloping embryo, a dry or rehydrated or freshly excised embryo), andcallus.

In embodiments, the non-epidermal cell is diploid or polyploid. Inembodiments, the non-epidermal plant cell is haploid or can be inducedto become haploid; techniques for making and using haploid plants andplant cells are known in the art, see, e. g., methods for generatinghaploids in Arabidopsis thaliana by crossing of a wild-type strain to ahaploid-inducing strain that expresses altered forms of thecentromere-specific histone CENH3, as described by Maruthachalam andChan in “How to make haploid Arabidopsis thaliana”, a protocol publiclyavailable atwww[dot]openwetware[dot]org/images/d/d3/Haploid_Arabidopsis_protocol[dot]pdf;Ravi et al. (2014) Nature Communications, 5:5334, doi:10.1038/ncomms6334). Examples of haploid cells include but are notlimited to plant cells in haploid plants and plant cells in reproductivetissues, e. g., flowers, developing flowers or flower buds, ovaries,ovules, megaspores, anthers, pollen, and microspores. In embodimentswhere the non-epidermal plant cell is haploid, the method can furtherinclude the step of chromosome doubling (e. g., by spontaneouschromosomal doubling by meiotic non-reduction, or by using a chromosomedoubling agent such as colchicine, oryzalin, or trifluralin) in thenon-epidermal plant cell including the altered target nucleotidesequence to produce a doubled haploid cell that is homozygous for thealtered target nucleotide sequence; yet other embodiments includeregeneration of a doubled haploid plant from the doubled haploid cell,wherein the regenerated doubled haploid plant is homozygous for thealtered target nucleotide sequence. Thus, aspects of the invention arerelated to the haploid cell having the altered target nucleotidesequence as well as a doubled haploid cell or a doubled haploid plantthat is homozygous for the altered target nucleotide sequence. Anotheraspect of the invention is related to a hybrid plant having at least oneparent plant that is a doubled haploid plant provided by the method.Production of doubled haploid plants by these methods provideshomozygosity in one generation, instead of requiring several generationsof self-crossing to obtain homozygous plants; this may be particularlyadvantageous in slow-growing plants, such as fruit and other trees, orfor producing hybrid plants that are offspring of at least onedoubled-haploid plant.

In embodiments, the plant is a dicot or a monocot. In embodiments, theplant is a gymnosperm, such as a conifer. Plants of interest include rowcrop plants, fruit-producing plants and trees, vegetables, trees, andornamental plants including ornamental flowers, shrubs, trees,groundcovers, and turf grasses. Examples of commercially importantcultivated crops, trees, and plants include: alfalfa (Medicago sativa),almonds (Prunus dulcis), apples (Malus x domestica), apricots (Prunusarmeniaca, P. brigantine, P. mandshurica, P. mume, P. sibirica),asparagus (Asparagus officinalis), bananas (Musa spp.), barley (Hordeumvulgare), beans (Phaseolus spp.), blueberries and cranberries (Vacciniumspp.), cacao (Theobroma cacao), canola and rapeseed or oilseed rape,(Brassica napus), carnation (Dianthus caryophyllus), carrots (Daucuscarota sativus), cassava (Manihot esculentum), cherry (Prunus avium),chickpea (Cider arietinum), chicory (Cichorium intybus), chili peppersand other capsicum peppers (Capsicum annuum, C. frutescens, C. chinense,C. pubescens, C. baccatum), chrysanthemums (Chrysanthemum spp.), coconut(Cocos nucifera), coffee (Coffea spp. including Coffea arabica andCoffea canephora), cotton (Gossypium hirsutum L.), cowpea (Vignaunguiculata), cucumber (Cucumis sativus), currants and gooseberries(Ribes spp.), eggplant or aubergine (Solanum melongena), eucalyptus(Eucalyptus spp.), flax (Linum usitatissumum L.), geraniums (Pelargoniumspp.), grapefruit (Citrus x paradisi), grapes (Vitus spp.) includingwine grapes (Vitus vinifera), guava (Psidium guajava), irises (Irisspp.), lemon (Citrus limon), lettuce (Lactuca sativa), limes (Citrusspp.), maize (Zea mays L.), mango (Mangifera indica), mangosteen(Garcinia mangostana), melon (Cucumis melo), millets (Setaria spp,Echinochloa spp, Eleusine spp, Panicum spp., Pennisetum spp.), oats(Avena sativa), oil palm (Ellis quineensis), olive (Olea europaea),onion (Allium cepa), orange (Citrus sinensis), papaya (Carica papaya),peaches and nectarines (Prunus persica), pear (Pyrus spp.), pea (Pisasativum), peanut (Arachis hypogaea), peonies (Paeonia spp.), petunias(Petunia spp.), pineapple (Ananas comosus), plantains (Musa spp.), plum(Prunus domestica), poinsettia (Euphorbia pulcherrima), Polish canola(Brassica rapa), poplar (Populus spp.), potato (Solanum tuberosum),pumpkin (Cucurbita pepo), rice (Oryza sativa L.), roses (Rosa spp.),rubber (Hevea brasiliensis), rye (Secale cereale), safflower (Carthamustinctorius L), sesame seed (Sesame indium), sorghum (Sorghum bicolor),soybean (Glycine max L.), squash (Cucurbita pepo), strawberries(Fragaria spp., Fragaria x ananassa), sugar beet (Beta vulgaris),sugarcanes (Saccharum spp.), sunflower (Helianthus annus), sweet potato(Ipomoea batatas), tangerine (Citrus tangerina), tea (Camelliasinensis), tobacco (Nicotiana tabacum L.), tomato (Lycopersiconesculentum), tulips (Tulipa spp.), turnip (Brassica rapa rapa), walnuts(Juglans spp. L.), watermelon (Citrulus lanatus), wheat (Tritiumaestivum), and yams (Discorea spp.).

Embodiments of the method involve various treatments employed to deliverthe polynucleotide composition to the non-epidermal plant cell. Inembodiments, one or more treatments is employed to deliver thepolynucleotide composition into the non-epidermal plant cell, e. g.,through barriers such as a seed coat, a cell wall, a plasma membrane ornuclear envelope or other lipid bilayer, or through multiple cell layersor tissues. In an embodiment, the polynucleotide composition isdelivered directly, for example by direct contact of the polynucleotidecomposition with the non-epidermal plant cell. Polynucleotidecompositions in the form of a liquid, a solution, a suspension, anemulsion, a reverse emulsion, a colloid, a dispersion, a gel, liposomes,micelles, an injectable material, an aerosol, a solid, a powder, aparticulate, a nanoparticle, or a combination thereof can be applieddirectly to a plant or plant part, to the surface or to the interior (e.g., through an incision, abrasion, or puncture, by spraying or dippingor soaking or otherwise directly contacting, by injection ormicroinjection). For example, a seed or seed fragment or embryo issoaked in or imbibes a liquid polynucleotide composition, whereby thegRNA is delivered to non-epidermal cells in the seed or seed fragment orembryo. In embodiments, the polynucleotide composition is deliveredusing negative or positive pressure, for example, using vacuuminfiltration or application of hydrodynamic or fluid pressure. Inembodiments, the polynucleotide composition is introduced into thevascular system of a plant or plant part, e. g., by injection ormicroinjection into the phloem, or by vascular uptake through a stem orpetiole; see, e. g., Sun et al. (2005) Plant J., 44:128-138. Inembodiments, the polynucleotide composition is introduced intonon-vascular tissues by injection or microinjection or through theapplication of negative or positive pressure. Other techniques usefulfor delivering the polynucleotide composition to a non-epidermal plantcell include: ultrasound or sonication; vibration, friction, shearstress, vortexing, cavitation; centrifugation or application ofmechanical force; mechanical cell wall or cell membrane deformation orbreakage; enzymatic cell wall or cell membrane breakage orpermeabilization; abrasion or mechanical scarification (e. g., abrasionwith carborundum or other particulate abrasive or scarification with afile or sandpaper) or chemical scarification (e. g., treatment with anacid or caustic agent); and electroporation. In embodiments, thepolynucleotide composition is provided by bacterially mediated (e. g.,Agrobacterium sp., Rhizobium sp., Sinorhizobium sp., Mesorhizobium sp.,Bradyrhizobium sp., Azobacter sp., Phyllobacterium sp.) transfection ofthe non-epidermal plant cell with a polynucleotide encoding the gRNA;see, e. g., Broothaerts et al. (2005) Nature, 433:629-633.

In embodiments, a treatment employed in delivery of the polynucleotidecomposition to the non-epidermal plant cell is carried out under aspecific thermal regime, which can involve one or more appropriatetemperatures, e. g., chilling or cold stress (exposure to temperaturesbelow that at which normal plant growth occurs), or heating or heatstress (exposure to temperatures above that at which normal plant growthoccurs), or treating at a combination of different temperatures. Inembodiments, a specific thermal regime is carried out on thenon-epidermal plant cell, or on the plant or plant part in which thenon-epidermal plant cell is located, in one or more steps separate fromthe polynucleotide composition delivery.

Delivery Agents:

Embodiments of the method include treatment of the non-epidermal plantcell, or the plant or plant part in which the non-epidermal plant cellis located, with one or more delivery agents which can include at leastone chemical, enzymatic, or physical agent, or a combination thereof. Inembodiments, the polynucleotide composition further includes one or moreone chemical, enzymatic, or physical agent for delivery. In embodimentsof the method that further include the step of providing to thenon-epidermal plant cell an RNA-guided nuclease or a polynucleotide thatencodes the RNA-guided nuclease, a composition including the RNA-guidednuclease or polynucleotide that encodes the RNA-guided nuclease furtherincludes one or more one chemical, enzymatic, or physical agent fordelivery. Treatment with the chemical, enzymatic or physical agent canbe carried out simultaneously with the polynucleotide compositiondelivery, with the RNA-guided nuclease delivery, or in one or moreseparate steps that precede or follow the polynucleotide compositiondelivery or the RNA-guided nuclease delivery. In embodiments, achemical, enzymatic, or physical agent, or a combination of these, isassociated or complexed with the polynucleotide composition, with thegRNA or polynucleotide that encodes or is processed to the gRNA, or withthe RNA-guided nuclease or polynucleotide that encodes the RNA-guidednuclease; examples of such associations or complexes include thoseinvolving non-covalent interactions (e. g., ionic or electrostaticinteractions, hydrophobic or hydrophilic interactions, formation ofliposomes, micelles, or other heterogeneous composition) and covalentinteractions (e. g., peptide bonds, bonds formed using cross-linkingagents). In non-limiting examples, a gRNA or polynucleotide that encodesor is processed to the gRNA is provided as a liposomal complex with acationic lipid; a gRNA or polynucleotide that encodes or is processed tothe gRNA is provided as a complex with a carbon nanotube; and anRNA-guided nuclease is provided as a fusion protein between the nucleaseand a cell-penetrating peptide. Examples of agents useful for deliveringa gRNA or polynucleotide that encodes or is processed to the gRNA or anuclease or polynucleotide that encodes the nuclease include the variouscationic liposomes and polymer nanoparticles reviewed by Zhang et al.(2007) J. Controlled Release, 123:1-10, and the cross-linkedmultilamellar liposomes described in US Patent Application Publication2014/0356414 A1, incorporated by reference in its entirety herein.

In embodiments, the chemical agent is at least one selected from thegroup consisting of:

(a) solvents (e. g., water, dimethylsulfoxide, dimethylformamide,acetonitrile, N-pyrrolidine, pyridine, hexamethylphosphoramide,alcohols, alkanes, alkenes, dioxanes, polyethylene glycol, and othersolvents miscible or emulsifiable with water or that will dissolvephosphonucleotides in non-aqueous systems);

(b) fluorocarbons (e. g., perfluorodecalin, perfluoromethyldecalin);

(c) glycols or polyols (e. g., propylene glycol, polyethylene glycol);

(d) surfactants, including cationic surfactants, anionic surfactants,non-ionic surfactants, and amphiphilic surfactants, e. g., alkyl or arylsulfates, phosphates, sulfonates, or carboxylates; primary, secondary,or tertiary amines; quaternary ammonium salts; sultaines, betaines;cationic lipids; phospholipids; tallowamine; bile acids such as cholicacid; saponins or glycosylated triterpenoids or glycosylated sterols (e.g., saponin commercially available as catalogue number 47036-500g-F,Sigma-Aldrich, St. Louis, Mo.); long chain alcohols; organosiliconesurfactants including nonionic organosilicone surfactants such astrisiloxane ethoxylate surfactants or a silicone polyether copolymersuch as a copolymer of polyalkylene oxide modified heptamethyltrisiloxane and allyloxypolypropylene glycol methylether (commerciallyavailable as SILWET L-77™ brand surfactant having CAS Number 27306-78-1and EPA Number CAL. REG. NO. 5905-50073-AA, Momentive PerformanceMaterials, Inc., Albany, N.Y.); specific examples of useful surfactantsinclude sodium lauryl sulfate, the Tween series of surfactants,Triton-X100, Triton-X114, CHAPS and CHAPSO, Tergitol-type NP-40, NonidetP-40;

(e) lipids, lipoproteins, lipopolysaccharides;

(f) acids, bases, caustic agents;

(g) peptides, proteins, or enzymes (e. g., cellulase, pectolyase,maceroenzyme, pectinase), including cell-penetrating or pore-formingpeptides (e. g., (BO100)2K8, Genscript; poly-lysine, poly-arginine, orpoly-homoarginine peptides; gamma zein, see US Patent Applicationpublication 2011/0247100, incorporated herein by reference in itsentirety; transcription activator of human immunodeficiency virus type 1(“HIV-1 Tat”) and other Tat proteins, see, e. g.,www[dot]lifetein[dot]com/Cell_Penetrating_Peptides[dot]html and Jarver(2012) Mol. Therapy—Nucleic Acids, 1:e27,1-17); octa-arginine ornona-arginine; poly-homoarginine (see Unnamalai et al. (2004) FEBSLetters, 566:307-310); see also the database of cell-penetratingpeptides CPPsite 2.0 publicly available atcrdd[dot]osdd[dot]net/raghava/cppsite/

(h) RNase inhibitors;

(i) cationic branched or linear polymers such as chitosan, poly-lysine,DEAE-dextran, polyvinylpyrrolidone (“PVP”), or polyethylenimine (“PEI”,e. g., PEI, branched, MW 25,000, CAS#9002-98-6; PEI, linear, MW 5000,CAS#9002-98-6; PEI linear, MW 2500, CAS#9002-98-6);

(j) dendrimers (see, e. g., US Patent Application Publication2011/0093982, incorporated herein by reference in its entirety);

(k) counter-ions, amines or polyamines (e. g., spermine, spermidine,putrescine), osmolytes, buffers, and salts (e. g., calcium phosphate,ammonium phosphate);

(l) polynucleotides (e. g., non-specific double-stranded DNA, salmonsperm DNA);

(m) transfection agents (e. g., Lipofectin®, Lipofectamine®, andOligofectamine®, and Invivofectamine® (all from Thermo FisherScientific, Waltham, Mass.), PepFect (see Ezzat et al. (2011) NucleicAcids Res., 39:5284-5298), TransIt® transfection reagents (Mirus Bio,LLC, Madison, Wis.), and poly-lysine, poly-homoarginine, andpoly-arginine molecules including octo-arginine and nono-arginine asdescribed in Lu et al. (2010) J. Agric. Food Chem., 58:2288-2294);

(n) antibiotics, including non-specific DNA double-strand-break-inducingagents (e. g., phleomycin, bleomycin, talisomycin);

(o) antioxidants (e. g., glutathione, dithiothreitol, ascorbate); and

(p) chelating agents (e. g., EDTA, EGTA).

In embodiments, the chemical agent is provided simultaneously with thegRNA (or polynucleotide encoding the gRNA or that is processed to thegRNA), for example, the polynucleotide composition including the gRNAfurther includes one or more chemical agent. In embodiments, the gRNA orpolynucleotide encoding the gRNA or that is processed to the gRNA iscovalently or non-covalently linked or complexed with one or morechemical agent; for example, the gRNA or polynucleotide encoding thegRNA or that is processed to the gRNA can be covalently linked to apeptide or protein (e. g., a cell-penetrating peptide or a pore-formingpeptide) or non-covalently complexed with cationic lipids, polycations(e. g., polyamines), or cationic polymers (e. g., PEI). In embodiments,the gRNA or polynucleotide encoding the gRNA or that is processed to thegRNA is complexed with one or more chemical agents to form, e. g., asolution, liposome, micelle, emulsion, reverse emulsion, suspension,colloid, or gel.

In embodiments, the physical agent is at least one selected from thegroup consisting of particles or nanoparticles (e. g., particles ornanoparticles made of materials such as carbon, silicon, siliconcarbide, gold, tungsten, polymers, or ceramics) in various size rangesand shapes, magnetic particles or nanoparticles (e. g., silenceMagMagnetotransfection™ agent, OZ Biosciences, San Diego, Calif.), abrasiveor scarifying agents, needles or microneedles, matrices, and grids. Inembodiments, particulates and nanoparticulates are useful in delivery ofthe polynucleotide composition or the nuclease or both. Usefulparticulates and nanoparticles include those made of metals (e. g.,gold, silver, tungsten, iron, cerium), ceramics (e. g., aluminum oxide,silicon carbide, silicon nitride, tungsten carbide), polymers (e. g.,polystyrene, polydiacetylene, and poly(3,4-ethylenedioxythiophene)hydrate), semiconductors (e. g., quantum dots), silicon (e. g., siliconcarbide), carbon (e. g., graphite, graphene, graphene oxide, or carbonnanosheets, nanocomplexes, or nanotubes), and composites (e. g.,polyvinylcarbazole/graphene, polystyrene/graphene, platinum/graphene,palladium/graphene nanocomposites). In embodiments, such particulatesand nanoparticulates are further covalently or non-covalentlyfunctionalized, or further include modifiers or cross-linked materialssuch as polymers (e. g., linear or branched polyethylenimine,poly-lysine), polynucleotides (e. g., DNA or RNA), polysaccharides,lipids, polyglycols (e. g., polyethylene glycol, thiolated polyethyleneglycol), polypeptides or proteins, and detectable labels (e. g., afluorophore, an antigen, an antibody, or a quantum dot). In variousembodiments, such particulates and nanoparticles are neutral, or carry apositive charge, or carry a negative charge. Embodiments of compositionsincluding particulates include those formulated, e. g., as liquids,colloids, dispersions, suspensions, aerosols, gels, and solids.Embodiments include nanoparticles affixed to a surface or support, e.g., an array of carbon nanotubes vertically aligned on a silicon orcopper wafer substrate. Embodiments include polynucleotide compositionsincluding particulates (e. g., gold or tungsten or magneticmicroparticles or nanoparticles) delivered by a Biolistic-type techniqueor with magnetic force. The size of the particles used in Biolistics isgenerally in the “microparticle” range, for example, gold microcarriersin the 0.6, 1.0, and 1.6 micrometer size ranges (see, e. g., instructionmanual for the Helios® Gene Gun System, Bio-Rad, Hercules, Calif.;Randolph-Anderson et al. (2015) “Sub-micron gold particles are superiorto larger particles for efficient Biolistic® transformation oforganelles and some cell types”, Bio-Rad US/EG Bulletin 2015), butsuccessful Biolistics delivery using larger (40 nanometer) nanoparticleshas been reported in cultured animal cells; see O'Brian and Lummis(2011) BMC Biotechnol., 11:66-71. Other embodiments of usefulparticulates are nanoparticles, which are generally in the nanometer(nm) size range or less than 1 micrometer, e. g., with a diameter ofless than about 1 nm, less than about 3 nm, less than about 5 nm, lessthan about 10 nm, less than about 20 nm, less than about 40 nm, lessthan about 60 nm, less than about 80 nm, and less than about 100 nm.Specific, non-limiting embodiments of nanoparticles commerciallyavailable (all from Sigma-Aldrich Corp., St. Louis, Mo.) include goldnanoparticles with diameters of 5, 10, or 15 nm; silver nanoparticleswith particle sizes of 10, 20, 40, 60, or 100 nm; palladium “nanopowder”of less than 25 nm particle size; single-, double-, and multi-walledcarbon nanotubes, e. g., with diameters of 0.7-1.1, 1.3-2.3, 0.7-0.9, or0.7-1.3 nm, or with nanotube bundle dimensions of 2-10 nm by 1-5micrometers, 6-9 nm by 5 micrometers, 7-15 nm by 0.5-10 micrometers,7-12 nm by 0.5-10 micrometers, 110-170 nm by 5-9 micrometers, 6-13 nm by2.5-20 micrometers. Embodiments include polynucleotide compositionsincluding materials such as gold, silicon, cerium, or carbon, e. g.,gold or gold-coated nanoparticles, silicon carbide whiskers,carborundum, porous silica nanoparticles, gelatin/silica nanoparticles,nanoceria or cerium oxide nanoparticles (CNPs), carbon nanotubes (CNTs)such as single-, double-, or multi-walled carbon nanotubes and theirchemically functionalized versions (e. g., carbon nanotubesfunctionalized with amide, amino, carboxylic acid, sulfonic acid, orpolyethylene glycol moeities), and graphene or graphene oxide orgraphene complexes; see, for example, Wong et al. (2016) Nano Lett.,16:1161-1172; Giraldo et al. (2014) Nature Materials, 13:400-409; Shenet al. (2012) Theranostics, 2:283-294; Kim et al. (2011) BioconjugateChem., 22:2558-2567; Wang et al. (2010) J. Am. Chem. Soc. Comm.,132:9274-9276; Zhao et al. (2016) Nanoscale Res. Lett., 11:195-203; Choiet al. (2016) J. Controlled Release, 235:222-235; and Zhai et al. (2014)Environ. Sci. Technol. Lett., 1:146-151. See also, for example, thevarious types of particles and nanoparticles, their preparation, andmethods for their use, e. g., in delivering polynucleotides andpolypeptides to cells, disclosed in US Patent Application Publications2010/0311168, 2012/0023619, 2012/0244569, 2013/0145488, 2013/0185823,2014/0096284, 2015/0040268, 2015/0047074, and 2015/0208663, all of whichare incorporated herein by reference in their entirety.

In embodiments wherein the polynucleotide composition includes anRNA-guided nuclease, or a polynucleotide that encodes the RNA-guidednuclease, or wherein the method further includes the step of providingto the non-epidermal plant cell an RNA-guided nuclease or apolynucleotide that encodes the RNA-guided nuclease, one or more onechemical, enzymatic, or physical agent can similarly be employed. Inembodiments, the RNA-guided nuclease (or polynucleotide encoding theRNA-guided nuclease) is provided separately, e. g., in a separatecomposition including the RNA-guided nuclease or polynucleotide encodingthe RNA-guided nuclease. Such compositions can include other chemical orphysical agents (e. g., solvents, surfactants, proteins or enzymes,transfection agents, particulates or nanoparticulates), such as thosedescribed above as useful in the polynucleotide composition used toprovide the gRNA. For example, porous silica nanoparticles are usefulfor delivering a DNA recombinase into maize cells; see, e. g.,Martin-Ortigosa et al. (2015) Plant Physiol., 164:537-547. In anembodiment, the polynucleotide composition includes a gRNA and Cas9nuclease, and further includes a surfactant and a cell-penetratingpeptide. In an embodiment, the polynucleotide composition includes aplasmid that encodes both an RNA-guided nuclease and at least on gRNA,and further includes a surfactant and carbon nanotubes. In anembodiment, the polynucleotide composition includes multiple gRNAs andan mRNA encoding the RNA-guided nuclease, and further includes goldparticles, and the polynucleotide composition is delivered to the plantcell by Biolistics.

In related embodiments, one or more one chemical, enzymatic, or physicalagent can be used in one or more steps separate from (preceding orfollowing) that in which the polynucleotide composition is provided tothe non-epidermal plant cell. In an embodiment, the plant or plant partin which the non-epidermal plant cell is located is treated with anagent to assist in access to the interior of the plant or plant part,for example, with an abrasive, a caustic agent, a surfactant, or anenzyme, followed by application of the polynucleotide composition (andoptionally the nuclease). In an embodiment, a halved seed or dissectedembryo is treated with a surfactant such as Silwet L-77, followed byapplication of the polynucleotide composition (and optionally thenuclease). In an embodiment, the shoot apical meristem of a plant istreated with cellulase, followed by application of the polynucleotidecomposition.

In embodiments, the polynucleotide composition is provided/applied at alocation in the plant or plant part other than the non-epidermal plantcell. In embodiments, the polynucleotide composition is applied toadjacent or distal non-meristematic cells and is transported (e. g.,through the vascular system or by cell-to-cell movement) to meristematicnon-epidermal plant cell. In embodiments, the polynucleotide compositionis applied by soaking a seed or seed fragment or embryo in thepolynucleotide composition, whereby the gRNA is delivered tonon-epidermal cells in the seed or seed fragment or embryo. Inembodiments, a flower bud or shoot tip is contacted with thepolynucleotide composition, whereby the gRNA is delivered tonon-epidermal cells in the flower bud or shoot tip, or to othernon-epidermal cells in the plant. In embodiments, the polynucleotidecomposition is applied to the surface of a plant or of a part of a plant(e. g., a leaf surface), whereby the gRNA is delivered to non-epidermalcells in the plant. In embodiments a whole plant or plant tissue issubjected to particle- or nanoparticle-mediated delivery (e. g.,Biolistics or carbon nanotube or nanoparticle delivery) of thepolynucleotide composition, whereby the gRNA is delivered tonon-epidermal plant cells.

Delivery of a gRNA by the method of the invention results in alterationof the target nucleotide sequence in the non-epidermal plant cell. Inembodiments, the altered target nucleotide sequence includes at leastone sequence modification selected from the group consisting ofinsertion of a nucleotide, deletion of a nucleotide, and replacement ofa nucleotide. In embodiments, insertion of a nucleotide includesinsertion of additional heterologous sequence. In embodiments,alteration of the target nucleotide sequence results in a change (e. g.,increase or decrease or change in temporal or spatial specificity) inexpression of the target nucleotide sequence, methylation ordemethylation of the target nucleotide sequence (e. g., resulting in anepigenetic change), or a phenotype, or a combination of these. Inembodiments, alteration of the target nucleotide sequence results in aphenotype or trait of interest observable in a seedling or plant grownor regenerated from the non-epidermal plant cell; in some embodimentsthe phenotype or trait is heritable to succeeding generations of plants.Thus, related embodiments include such succeeding generations of plantsor their seeds having inherited the altered target nucleotide sequence.

A related aspect of the invention is directed to the non-epidermal plantcell including an altered target nucleotide sequence, provided by themethod. Embodiments of the method further include one or more steps ofgrowing or regenerating a plant from the non-epidermal plant cellincluding an altered target nucleotide sequence, wherein the grown orregenerated plant contains at least some cells or tissues having thealtered target nucleotide sequence. In embodiments, callus is producedfrom the non-epidermal plant cell, and plantlets and plants producedfrom such callus. In other embodiments, whole seedlings or plants aregrown directly from the non-epidermal plant cell without a callus stage.Thus, additional related aspects are directed to whole seedlings andplants grown or regenerated from the non-epidermal plant cell includingan altered target nucleotide sequence, as well as the seeds of suchplants. In embodiments, the grown or regenerated plant exhibits aphenotype associated with the altered target nucleotide sequence. Inembodiments, the grown or regenerated plant includes in its genome twoor more genetic modifications that in combination provide at least onephenotype of interest, wherein at least one genetic modificationincludes the altered target nucleotide sequence in the non-epidermalplant cell. In embodiments, a heterogeneous population of non-epidermalplant cells, at least some of which include one or more altered targetnucleotide sequences, is provided by the method; related aspects includea plant having a phenotype of interest associated with the alteredtarget nucleotide sequence, provided by either regeneration of a planthaving the phenotype of interest from a cell selected from theheterogeneous population of non-epidermal plant cells, or by selectionof a plant having the phenotype of interest from a heterogeneouspopulation of plants grown or regenerated from the population ofnon-epidermal plant cells. Examples of phenotypes of interest includeherbicide resistance, improved tolerance of abiotic stress (e. g.,tolerance of temperature extremes, drought, or salt) or biotic stress(e. g., resistance to bacterial or fungal pathogens), improvedutilization of nutrients or water, modified lipid, carbohydrate, orprotein composition, improved flavour or appearance, improved storagecharacteristics (e. g., resistance to bruising, browning, or softening),increased yield, altered morphology (e. g., floral architecture orcolour, plant height, branching, root structure). In an embodiment, aheterogeneous population of non-epidermal plant cells (or seedlings orplants grown or regenerated from the cells) is exposed to conditionspermitting expression of the phenotype of interest; e. g., selection forherbicide resistance can include exposing the population of cells (orseedlings or plants) to an amount of herbicide or other substance thatinhibits growth or is toxic, allowing identification and selection ofthose resistant cells (or seedlings or plants) that survive treatment.Also contemplated are heterogeneous populations, arrays, or libraries ofsuch plants, succeeding generations or seeds of such plants, parts ofthe plants (including plant parts used in grafting as scions orrootstocks), or products (e. g., fruits or other edible plant parts,cleaned grains or seeds, edible oils, flours or starches, proteins, andother processed products) made from the plants or their seeds.Embodiments include plants that contain cells or tissues that do nothave the altered nucleotide sequence, e. g., grafted plants in which thescion or rootstock contains the altered nucleotide sequence, or chimericplants in which some but not all cells or tissues contain the alterednucleotide sequence. Plants in which grafting is commonly useful includemany fruit trees and plants such as many citrus trees, apples, stonefruit (e. g., peaches, apricots, cherries, and plums), avocados,tomatoes, eggplant, cucumber, melons, watermelons, and grapes as well asvarious ornamental plants such as roses. Grafted plants can be graftsbetween the same or different (generally related) species. Additionalrelated aspects include a hybrid plant provided by crossing a firstplant grown or regenerated from a non-epidermal plant cell with analtered target nucleotide sequence, with a second plant, wherein thehybrid plant contains the altered target nucleotide sequence; alsocontemplated is seed produced by the hybrid plant.

Delivery of Effector Molecules to a Plant Cell

In related aspects, the delivery techniques, delivery agents, andcompositions disclosed above under the heading “Methods of altering atarget nucleotide sequence in a non-epidermal plant cell” are useful ingeneral for delivering other molecules to effect an alteration in anucleotide sequence in a plant cell capable of division anddifferentiation. Such “effector molecules” include other nucleases orpolynucleotides encoding a nuclease capable of effecting site-specificalteration of a target nucleotide sequence, and guide polynucleotidesthat guide nucleases in a sequence-specific manner to a targetnucleotide sequence.

Thus, a related aspect of the invention is a method of providing a planthaving a genetic alteration, including: (a) delivery of at least oneeffector molecule to a plant cell capable of division anddifferentiation, resulting in a genetic alteration of the plant cell,wherein the plant cell is a cell in a plant or part of a plant selectedfrom the group consisting of a plant tissue, a whole plant, an intactnodal bud, a shoot apex or shoot apical meristem, a root apex or rootapical meristem, lateral meristem, intercalary meristem, a seedling (e.g., a germinating seed or small seedling or a larger seedling with oneor more true leaves), a whole seed (e. g., an intact seed, or a seedwith part or all of its seed coat removed or treated to make permeable),a halved seed or other seed fragment, an embryo (e. g., a maturedissected zygotic embryo, a developing embryo, a dry or rehydrated orfreshly excised embryo), and callus; wherein the delivery of the atleast one effector molecule includes at least one treatment selectedfrom the group consisting of: direct application; soaking or imbibition;vacuum infiltration; application of negative or positive pressure;introduction into the vascular system; microinjection; application ofultrasound or vibration; application of hydrodynamic pressure, friction,cavitation or shear stress; vortexing; centrifugation; mechanical cellwall or cell membrane deformation or breakage; enzymatic cell wall orcell membrane breakage or permeabilization; abrasion; electroporation;and treatment with at least one chemical, enzymatic, or physical agent;and (b) regeneration of a plant from the plant cell having the geneticalteration, wherein the plant includes differentiated cells or tissueshaving the genetic alteration. In embodiments, delivery of the at leastone effector molecule alters a target nucleotide sequence in the plantcell, resulting in a genetic alteration such as insertion of anucleotide, deletion of a nucleotide, or replacement of a nucleotide. Inembodiments, insertion of a nucleotide includes insertion of additionalheterologous sequence. In embodiments, the genetic alteration results ina change (e. g., increase or decrease or change in temporal or spatialspecificity) in expression of the target nucleotide sequence,methylation or demethylation of the target nucleotide sequence (e. g.,resulting in an epigenetic change), or a phenotype, or a combination ofthese.

The target nucleotide sequence is one or more nucleotide sequences,including protein-coding sequence or non-coding sequence or acombination thereof. Embodiments include a plant nuclear sequence, aplant plastid sequence, a plant mitochondrial sequence, a sequence of asymbiont, pest, or pathogen of a plant, and combinations thereof. Inembodiments, multiple target nucleotide sequences are altered, forexample, by delivery of multiple effector molecules to the plant cell;the multiple target nucleotide sequences can be part of the same gene(e. g., different locations in a single coding region or in differentexons of a protein-coding gene) or different genes.

Embodiments of effector molecules include: (a) a polynucleotide selectedfrom the group consisting of an RNA guide for an RNA-guided nuclease, aDNA encoding an RNA guide for an RNA-guided nuclease; (b) a nucleaseselected from the group consisting of an RNA-guided nuclease, anRNA-guided DNA endonuclease, a type II Cas nuclease, a Cas9, a type VCas nuclease, a Cpf1, a CasY, a CasX, a C2c1, a C2c3, an engineerednuclease, a codon-optimized nuclease, a zinc-finger nuclease (ZFN), atranscription activator-like effector nuclease (TAL-effector nuclease),Argonaute, a meganuclease or engineered meganuclease; or (c) apolynucleotide encoding one or more nucleases capable of effectingsite-specific alteration of a target nucleotide sequence. Any of thesenucleases can be codon-optimized, e. g., plant-codon-optimized tofunction optimally in a plant cell. In embodiments, one or multipleeffector molecules are delivered individually (e. g., in separatecompositions) or in combinations (e. g., in a ribonucleoprotein), and ina single step or multiple steps.

Zinc finger nucleases (ZFNs) are engineered proteins including a zincfinger DNA-binding domain fused to a nucleic acid cleavage domain, e.g., a nuclease. The zinc finger binding domains provide specificity andcan be engineered to specifically recognize any desired target DNAsequence. For a review of the construction and use of ZFNs in plants andother organisms, see, e. g., Urnov et al. (2010) Nature Rev. Genet.,11:636-646. The zinc finger DNA binding domains are derived from theDNA-binding domain of a large class of eukaryotic transcription factorscalled zinc finger proteins (ZFPs). The DNA-binding domain of ZFPstypically contains a tandem array of at least three zinc “fingers” eachrecognizing a specific triplet of DNA. A number of strategies can beused to design the binding specificity of the zinc finger bindingdomain. One approach, termed “modular assembly”, relies on thefunctional autonomy of individual zinc fingers with DNA. In thisapproach, a given sequence is targeted by identifying zinc fingers foreach component triplet in the sequence and linking them into amultifinger peptide. Several alternative strategies for designing zincfinger DNA binding domains have also been developed. These methods aredesigned to accommodate the ability of zinc fingers to contactneighboring fingers as well as nucleotides bases outside their targettriplet. Typically, the engineered zinc finger DNA binding domain has anovel binding specificity, compared to a naturally-occurring zinc fingerprotein. Engineering methods include, for example, rational design andvarious types of selection. Rational design includes, for example, theuse of databases of triplet (or quadruplet) nucleotide sequences andindividual zinc finger amino acid sequences, in which each triplet orquadruplet nucleotide sequence is associated with one or more amino acidsequences of zinc fingers which bind the particular triplet orquadruplet sequence. See, e. g., U.S. Pat. Nos. 6,453,242 and 6,534,261,both incorporated herein by reference in their entirety. Exemplaryselection methods (e. g., phage display and yeast two-hybrid systems)are well known and described in the literature. In addition, enhancementof binding specificity for zinc finger binding domains has beendescribed in U.S. Pat. No. 6,794,136, incorporated herein by referencein its entirety. In addition, individual zinc finger domains may belinked together using any suitable linker sequences. Examples of linkersequences are publicly known, e. g., see U.S. Pat. Nos. 6,479,626;6,903,185; and 7,153,949, incorporated herein by reference in theirentirety. The nucleic acid cleavage domain is non-specific and istypically a restriction endonuclease, such as Fok1. This endonucleasemust dimerize to cleave DNA. Thus, cleavage by Fok1 as part of a ZFNrequires two adjacent and independent binding events, which must occurin both the correct orientation and with appropriate spacing to permitdimer formation. The requirement for two DNA binding events enables morespecific targeting of long and potentially unique recognition sites.Fold variants with enhanced activities have been described; see, e. g.,Guo et al. (2010) J. Mol. Biol., 400:96-107.

Transcription activator like effectors (TALEs) are proteins secreted bycertain Xanthomonas species to modulate gene expression in host plantsand to facilitate the colonization by and survival of the bacterium.TALEs act as transcription factors and modulate expression of resistancegenes in the plants. Recent studies of TALEs have revealed the codelinking the repetitive region of TALEs with their target DNA-bindingsites. TALEs comprise a highly conserved and repetitive regionconsisting of tandem repeats of mostly 33 or 34 amino acid segments. Therepeat monomers differ from each other mainly at amino acid positions 12and 13. A strong correlation between unique pairs of amino acids atpositions 12 and 13 and the corresponding nucleotide in the TALE-bindingsite has been found. The simple relationship between amino acid sequenceand DNA recognition of the TALE binding domain allows for the design ofDNA binding domains of any desired specificity. TALEs can be linked to anon-specific DNA cleavage domain to prepare genome editing proteins,referred to as TAL-effector nucleases or TALENs. As in the case of ZFNs,a restriction endonuclease, such as Fok1, can be conveniently used. Fora description of the use of TALENs in plants, see Mahfouz et al. (2011)Proc. Natl. Acad. Sci. USA, 108:2623-2628 and Mahfouz (2011) GM Crops,2:99-103.

Argonautes are proteins that can function as sequence-specificendonucleases by binding a polynucleotide (e. g., a single-stranded DNAor single-stranded RNA) that includes sequence complementary to a targetnucleotide sequence) that guides the Argonaut to the target nucleotidesequence and effects site-specific alteration of the target nucleotidesequence; see, e. g., US Patent Application Publication 2015/0089681,incorporated herein by reference in its entirety.

In related embodiments, zinc finger nucleases, TALENs, and Argonautesare used in conjunction with other functional domains. For example, thenuclease activity of these nucleic acid targeting systems can be alteredso that the enzyme binds to but does not cleave the DNA. Examples offunctional domains include transposase domains, integrase domains,recombinase domains, resolvase domains, invertase domains, proteasedomains, DNA methyltransferase domains, DNA hydroxylmethylase domains,DNA demethylase domains, histone acetylase domains, histone deacetylasedomains, nuclease domains, repressor domains, activator domains,nuclear-localization signal domains, transcription-regulatory protein(or transcription complex recruiting) domains, cellular uptake activityassociated domains, nucleic acid binding domains, antibody presentationdomains, histone modifying enzymes, recruiter of histone modifyingenzymes; inhibitor of histone modifying enzymes, histonemethyltransferases, histone demethylases, histone kinases, histonephosphatases, histone ribosylases, histone deribosylases, histoneubiquitinases, histone deubiquitinases, histone biotinases and histonetail proteases. Non-limiting examples of functional domains include atranscriptional activation domain, a transcription repression domain,and an SHH1, SUVH2, or SUVH9 polypeptide capable of reducing expressionof a target nucleotide sequence via epigenetic modification; see, e. g.,US Patent Application Publication 2016/0017348, incorporated herein byreference in its entirety. Genomic DNA may also be modified via baseediting using a fusion between a catalytically inactive Cas9 (dCas9) isfused to a cytidine deaminase which convert cytosine (C) to uridine (U),thereby effecting a C to T substitution; see Komor et al. (2016) Nature,533:420-424.

In embodiments, the plant cell capable of division and differentiationis diploid or polyploid. In embodiments, the plant cell is haploid orcan be induced to become haploid; examples include but are not limitedto plant cells in haploid plants and plant cells in reproductivetissues, e. g., flowers, developing flowers or flower buds, ovaries,ovules, megaspores, anthers, pollen, and microspores. In embodimentswhere the plant cell is haploid, the method can further include the stepof chromosome doubling (e. g., by using a chromosome doubling agent suchas colchicine) in the plant cell including the genetic alteration toproduce a doubled haploid cell that is homozygous for the geneticalteration; yet other embodiments include regeneration of a doubledhaploid plant from the doubled haploid cell, wherein the regenerateddoubled haploid plant is homozygous for the genetic alteration. Thus,aspects of the invention are related to the haploid cell having thegenetic alteration as well as a doubled haploid cell or a doubledhaploid plant that is homozygous for the genetic alteration. Anotheraspect of the invention is related to a hybrid plant having at least oneparent plant that is a doubled haploid plant provided by the method.

A related aspect of the invention is directed to the plant having agenetic alteration, provided by the method. In embodiments, the plant isa monocot or a dicot, or is haploid, diploid, polyploid, or doubledhaploid. Embodiments include plants that contain cells or tissues thatdo not have the genetic alteration, e. g., grafted plants in which thescion or rootstock contains the genetic alteration, or chimeric plantsin which some but not all cells or tissues contain the geneticalteration. In embodiments, the genetic alteration is heritable tosucceeding generations; further aspects thus include seed and progenyplants of the plant having a genetic alteration, wherein the seed orprogeny plants contain the genetic alteration, as well as parts of suchseed or progeny plants (including plant parts used in grafting as scionsor rootstocks), or products (e. g., fruits or other edible plant parts,cleaned grains or seeds, edible oils, flours or starches, proteins, andother processed products) made from the seed or progeny plants. Inembodiments, callus is produced from the plant cell having the geneticalteration, and plantlets and plants produced from such callus. In otherembodiments, whole seedlings or plants are grown directly from the plantcell having the genetic alteration without a callus stage. Thus,additional related aspects are directed to whole seedlings and plantsgrown or regenerated from the plant cell having the genetic alteration,as well as the seeds of such plants. In embodiments, the grown orregenerated plant exhibits a phenotype associated with the geneticalteration. Examples of phenotypes of interest include herbicideresistance, improved tolerance of abiotic stress (e. g., tolerance oftemperature extremes, drought, or salt) or biotic stress (e. g.,resistance to bacterial or fungal pathogens), improved utilization ofnutrients or water, modified lipid, carbohydrate, or proteincomposition, improved flavour or appearance, increased yield, alteredmorphology (e. g., floral architecture, plant height, branching, rootstructure). In embodiments, the grown or regenerated plant includes inits genome two or more genetic modifications that in combination provideat least one phenotype of interest, wherein at least one geneticmodification includes the genetic alteration provided by the plant celltreated by the method.

Methods for Investigating Reverse Genetics

Another aspect of the invention is related to methods for investigatingreverse genetics, for example, a method of identifying a nucleotidesequence (or alteration of a nucleotide sequence, such as a nativenucleotide sequence) that is associated with a phenotype of interest. Inan embodiment, the method includes the steps of altering the genome of apopulation of plant cells (or plant protoplasts), optionally growing orregenerating a population of calli, seedlings, plantlets, or plants fromthe population of plant cells, and selecting the plant cells (or grownor regenerated calli, seedlings, plantlets, or plants) exhibiting thephenotype of interest and identifying the nucleotide sequence associatedwith the phenotype. Embodiments of the method include culturing orgrowing the plant cells or protoplasts (or calli, seedlings, plantlets,or plants) under conditions that permit expression of the phenotype ofinterest.

In an embodiment, the method includes the steps of: (a) contacting apopulation of plant cells (or protoplasts) with a library of gRNAs andoptionally with an RNA-guided DNA nuclease, whereby the genome of theplant cells is altered, culturing the population of plant cells underconditions that permit expression of the phenotype of interest,selecting the plant cells that exhibit the phenotype of interest, andidentifying the nucleotide sequence or alteration of a nucleotidesequence, wherein the nucleotide sequence thus identified is associatedwith the phenotype; or (b) contacting a population of plant cells (orprotoplasts) with a library of gRNAs and optionally with an RNA-guidedDNA nuclease, whereby the genome of the cells is altered, regenerating apopulation of plants from the population of plant cells, growing thepopulation of plants under conditions that permit expression of thephenotype of interest, selecting the plants that exhibit the phenotypeof interest, and identifying the nucleotide sequence or alteration of anucleotide sequence, wherein the nucleotide sequence thus identified isassociated with the phenotype. In embodiments, the plant cells in whichthe genome is altered are haploid cells (e. g., microspore or othergametophytic cells, or cells of a haploid plant) and the plantsregenerated from these cells are haploid plants; in embodiments themethod further includes the step of generating doubled-haploid cells ordoubled-haploid plants from the haploid cells or plants.

In embodiments, the gRNA is provided as a polynucleotide compositionincluding: (i) a CRISPR RNA (crRNA) that includes the gRNA, or apolynucleotide that encodes a crRNA, or a polynucleotide that isprocessed into a crRNA; or (ii) a single guide RNA (sgRNA) that includesthe gRNA, or a polynucleotide that encodes an sgRNA, or a polynucleotidethat is processed into an sgRNA. In embodiments, the plant cells containor express the appropriate RNA-guided DNA nuclease; in other embodimentsthe RNA-guided DNA nuclease, or a polynucleotide encoding the RNA-guidedDNA nuclease, is provided to the plant cells. In embodiments, thenuclease is selected from the group consisting of an RNA-guidednuclease, an RNA-guided DNA endonuclease, a type II Cas nuclease, aCas9, a type V Cas nuclease, a Cpf1, a CasY, a CasX, a C2c1, a C2c3, anengineered nuclease, a codon-optimized nuclease, a zinc-finger nuclease(ZFN), a transcription activator-like effector nuclease (TAL-effectornuclease), Argonaute, a meganuclease or engineered meganuclease. Methodsand compositions useful for delivering the library of gRNAs or theRNA-guided DNA nuclease are similar to those described under the heading“Methods of altering a target nucleotide sequence in a plant cell”.

Compositions and Reaction Mixtures

Another aspect of the invention is related to compositions and reactionsmixtures useful for carrying out methods such as those described herein.In one aspect, the invention is related to a composition or a reactionmixture including: (a) at least one non-epidermal plant cell, which inembodiments is a cell in whole plant, whole seed, embryo, plant part, orplant tissue; (b) at least one effector molecule for inducing a geneticalteration in the non-epidermal plant cell, wherein the at least oneeffector molecule is selected from the group consisting of: (i) apolynucleotide selected from the group consisting of an RNA guide for anRNA-guided nuclease, a DNA encoding an RNA guide for an RNA-guidednuclease; (ii) a nuclease selected from the group consisting of anRNA-guided nuclease, an RNA-guided DNA endonuclease, a type II Casnuclease, a Cas9, a type V Cas nuclease, a Cpf1, a CasY, a CasX, a C2c1,a C2c3, an engineered nuclease, a codon-optimized nuclease, azinc-finger nuclease (ZFN), a transcription activator-like effectornuclease (TAL-effector nuclease), Argonaute, a meganuclease orengineered meganuclease; or (iii) a polynucleotide encoding one or morenucleases capable of effecting site-specific alteration of a targetnucleotide sequence; and (c) optionally, at least one delivery agentselected from the group consisting of solvents, fluorocarbons, glycolsor polyols, surfactants; primary, secondary, or tertiary amines andquaternary ammonium salts; organosilicone surfactants; lipids,lipoproteins, lipopolysaccharides; acids, bases, caustic agents;peptides, proteins, or enzymes; cell-penetrating peptides; RNaseinhibitors; cationic branched or linear polymers; dendrimers;counter-ions, amines or polyamines, osmolytes, buffers, and salts;polynucleotides; transfection agents; antibiotics; non-specific DNAdouble-strand-break-inducing agents; antioxidants; chelating agents;particles or nanoparticles, magnetic particles or nanoparticles,abrasive or scarifying agents, needles or microneedles, matrices, andgrids.

In another aspect, the invention is related to a composition or areaction mixture including: (a) at least one non-epidermal plant cell,which in embodiments is a cell in whole plant, whole seed, embryo, plantpart, or plant tissue; (b) at least one guide RNA (gRNA) having anucleotide sequence designed to alter a target nucleotide sequence inthe non-epidermal plant cell, wherein the gRNA is provided as apolynucleotide composition including: (i) a CRISPR RNA (crRNA) thatincludes the gRNA, or a polynucleotide that encodes a crRNA, or apolynucleotide that is processed into a crRNA; or (ii) a single guideRNA (sgRNA) that includes the gRNA, or a polynucleotide that encodes ansgRNA, or a polynucleotide that is processed into an sgRNA; (c)optionally, at least one nuclease, or at least one polynucleotide thatencodes the nuclease, wherein the nuclease is selected from the groupconsisting of an RNA-guided nuclease, an RNA-guided DNA endonuclease, atype II Cas nuclease, a Cas9, a type V Cas nuclease, a Cpf1, a CasY, aCasX, a C2c1, a C2c3, an engineered nuclease, a codon-optimizednuclease, a zinc-finger nuclease (ZFN), a transcription activator-likeeffector nuclease (TAL-effector nuclease), Argonaute, a meganuclease orengineered meganuclease; and (d) optionally, at least one delivery agentselected from the group consisting of solvents, fluorocarbons, glycolsor polyols, surfactants; primary, secondary, or tertiary amines andquaternary ammonium salts; organosilicone surfactants; lipids,lipoproteins, lipopolysaccharides; acids, bases, caustic agents;peptides, proteins, or enzymes; cell-penetrating peptides; RNaseinhibitors; cationic branched or linear polymers; dendrimers;counter-ions, amines or polyamines, osmolytes, buffers, and salts;polynucleotides; transfection agents; antibiotics; non-specific DNAdouble-strand-break-inducing agents; antioxidants; chelating agents;particles or nanoparticles, magnetic particles or nanoparticles,abrasive or scarifying agents, needles or microneedles, matrices, andgrids. In embodiments, the gRNA is a single guide RNA (sgRNA) thatincludes the gRNA, wherein the composition further includes anRNA-guided nuclease, and wherein the sgRNA and RNA guided-nuclease areprovided as a ribonucleoprotein (RNP) complex. In embodiments, the atleast one plant cell or plant protoplast is a population of plant cellsor plant protoplasts, the at least one gRNA is two or more sgRNAs,wherein the composition further includes an RNA-guided nuclease, andwherein the two or more sgRNAs are each provided are provided as aribonucleoprotein (RNP) complex with the RNA guided-nuclease.

In embodiments of these compositions and reaction mixtures, the at leastone non-epidermal plant cell is a plant cell located in plant tissue, aplant part, or an intact plant or seed, or is a plant cell in callus. Inembodiments, the at least one non-epidermal plant cell is obtained froma monocot or a dicot. In various embodiments, the at least onenon-epidermal plant cell is haploid, diploid, or polyploid.

The foregoing description and the examples presented in this disclosuredescribe the subject matter of this invention, which includes thefollowing: (I) a method of delivering a guide RNA (gRNA) to anon-epidermal plant cell, wherein the non-epidermal plant cell is in aplant or part of a plant, wherein the gRNA has a nucleotide sequencedesigned to alter a target nucleotide sequence in the non-epidermalplant cell, and wherein the gRNA is provided as a polynucleotidecomposition including: (i) a CRISPR RNA (crRNA) that includes the gRNA,or a polynucleotide that encodes a crRNA, or a polynucleotide that isprocessed into a crRNA; or (ii) a single guide RNA (sgRNA) that includesthe gRNA, or a polynucleotide that encodes an sgRNA, or a polynucleotidethat is processed into an sgRNA; wherein the delivery of thepolynucleotide composition includes at least one treatment selected fromthe group consisting of: direct application; soaking or imbibition;vacuum infiltration; application of negative or positive pressure;introduction into the vascular system; microinjection; application ofultrasound or vibration; application of hydrodynamic pressure, friction,cavitation or shear stress; vortexing; centrifugation; mechanical cellwall or cell membrane deformation or breakage; enzymatic cell wall orcell membrane breakage or permeabilization; abrasion; electroporation;and treatment with at least one chemical, enzymatic, or physical agent;whereby the gRNA is delivered to the non-epidermal plant cell; whereinthe method is optionally further characterized by one or more of thefollowing: (1) wherein the plant or part of a plant is selected from thegroup consisting of a plant tissue, a whole plant, an intact nodal bud,a shoot apex or shoot apical meristem, a root apex or root apicalmeristem, lateral meristem, intercalary meristem, a seedling, a wholeseed, a halved seed or other seed fragment, an embryo, and callus; (2)wherein the plant is a dicot or a monocot; (3) wherein delivery of thegRNA results in alteration of the target nucleotide sequence in thenon-epidermal plant cell; (4) wherein: (a) the polynucleotidecomposition optionally includes an RNA-guided nuclease, or apolynucleotide that encodes the RNA-guided nuclease; or (b) the methodfurther includes the step of providing to the non-epidermal plant cellan RNA-guided nuclease or a polynucleotide that encodes the RNA-guidednuclease; or (c) the non-epidermal plant cell includes an RNA-guidednuclease or a polynucleotide that encodes the RNA-guided nuclease; (5)wherein (a) the polynucleotide composition further includes a chemicalagent or a physical agent or a combination of both chemical and physicalagents, or (b) the method further includes the step of treating theplant cell with a chemical agent or a physical agent or a combination ofboth chemical and physical agents; wherein the chemical agent is atleast one selected from the group consisting of solvents, fluorocarbons,glycols or polyols, surfactants; primary, secondary, or tertiary aminesand quaternary ammonium salts; saponins; organosilicone surfactants;lipids, lipoproteins, lipopolysaccharides; acids, bases, caustic agents;peptides, proteins, or enzymes; cell-penetrating peptides; RNaseinhibitors; cationic branched or linear polymers; dendrimers;counter-ions, amines or polyamines, osmolytes, buffers, and salts;polynucleotides; transfection agents; antibiotics; non-specific DNAdouble-strand-break-inducing agents; antioxidants; and chelating agents;and wherein the physical agent is at least one selected from the groupconsisting of particles or nanoparticles, magnetic particles ornanoparticles, abrasive or scarifying agents, needles or microneedles,matrices, and grids; (6) wherein the crRNA, the polynucleotide thatencodes a crRNA, the polynucleotide that is processed into a crRNA, thesgRNA, the polynucleotide that encodes an sgRNA, or the polynucleotidethat is processed into an sgRNA further includes one or more additionalnucleotide sequences selected from the group consisting of an aptamer orriboswitch sequence, a nucleotide sequence that provides secondarystructure, a nucleotide sequence that provides a sequence-specific sitefor an enzyme, T-DNA sequence, a DNA nuclear-targeting sequence, aregulatory sequence, and a transcript-stabilizing sequence; (7) whereinthe crRNA, the polynucleotide that encodes a crRNA, the polynucleotidethat is processed into a crRNA, the sgRNA, the polynucleotide thatencodes an sgRNA, or the polynucleotide that is processed into an sgRNAincludes: (a) double-stranded RNA, (b) single-stranded RNA; (c)chemically modified RNA; (d) a combination of (a)-(c); (8) wherein thepolynucleotide composition includes a liquid, a solution, a suspension,an emulsion, a reverse emulsion, a colloid, a dispersion, a gel,liposomes, micelles, an injectable material, an aerosol, a solid, apowder, a particulate, a nanoparticle, or a combination thereof; (9)wherein the polynucleotide composition is provided at a location in theplant or plant part other than the non-epidermal plant cell; (10)wherein: (a) the polynucleotide composition optionally includes anRNA-guided nuclease, or a polynucleotide that encodes the RNA-guidednuclease; or (b) the method further includes the step of providing tothe non-epidermal plant cell an RNA-guided nuclease or a polynucleotidethat encodes the RNA-guided nuclease; or (c) the non-epidermal plantcell includes an RNA-guided nuclease or a polynucleotide that encodesthe RNA-guided nuclease; and wherein the RNA-guided nuclease is selectedfrom the group consisting of an RNA-guided DNA endonuclease, a type IICas nuclease, a Cas9, a type V Cas nuclease, a Cpf1, a CasY, a CasX, aC2c1, a C2c3, an engineered nuclease, and a codon-optimized nuclease;(11) wherein: (a) the polynucleotide composition optionally includes anRNA-guided nuclease, or a polynucleotide that encodes the RNA-guidednuclease; or (b) the method further includes the step of providing tothe non-epidermal plant cell an RNA-guided nuclease or a polynucleotidethat encodes the RNA-guided nuclease; or (c) the non-epidermal plantcell includes an RNA-guided nuclease or a polynucleotide that encodesthe RNA-guided nuclease; and wherein the RNA-guided nuclease orpolynucleotide that encodes the RNA-guided nuclease is provided: (a) asa ribonucleoprotein complex including the crRNA and the RNA-guidednuclease; (b) as a complex including the RNA-guided nuclease orpolynucleotide that encodes the RNA-guided nuclease and at least onepeptide selected from the group consisting of a cell-penetratingpeptide, viral movement protein, or transfecting peptide; (c) as afusion protein including the RNA-guided nuclease and at least onepeptide selected from the group consisting of a cell-penetratingpeptide, viral movement protein, or transfecting peptide; (d) on acarrier molecule or a particulate; (e) in a liposome, micelle,protoplast or protoplast fragment; or (f) using a combination of any of(a)-(e); (12) wherein: (a) the polynucleotide composition optionallyincludes an RNA-guided nuclease, or a polynucleotide that encodes theRNA-guided nuclease; or (b) the method further includes the step ofproviding to the non-epidermal plant cell an RNA-guided nuclease or apolynucleotide that encodes the RNA-guided nuclease; or (c) thenon-epidermal plant cell includes an RNA-guided nuclease or apolynucleotide that encodes the RNA-guided nuclease; and wherein theRNA-guided nuclease is provided: (a) by contacting the non-epidermalplant cell with the RNA-guided nuclease or polynucleotide that encodesthe RNA-guided nuclease; (b) by transporting the RNA-guided nuclease orpolynucleotide that encodes the RNA-guided nuclease into thenon-epidermal plant cell using a chemical, enzymatic, or physical agent;(c) by bacterially mediated transfection with a polynucleotide encodingthe RNA-guided nuclease; or (d) by transcription of a polynucleotidethat encodes the RNA-guided nuclease; and (13) wherein the non-epidermalplant cell is: (a) diploid or (b) haploid.

The subject matter of this invention further includes: (II) Anon-epidermal plant cell including an altered target nucleotidesequence, provided by at least one of the methods described above under(I), wherein the method is optionally further characterized by furtherincluding growth or regeneration of a plant from the non-epidermal plantcell including an altered target nucleotide sequence, wherein the plantincludes cells having the altered target nucleotide sequence. Thesubject matter of this invention therefore further includes: (III) Aregenerated plant provided by at least one of the methods describedabove under (I), or seed or plant parts of the regenerated plant,wherein the method further includes growth or regeneration of a plantfrom the non-epidermal plant cell including an altered target nucleotidesequence, wherein the plant includes cells having the altered targetnucleotide sequence; and wherein the regenerated plant is optionallyfurther characterized by one or more of the following: (1) wherein theregenerated plant exhibits a phenotype associated with the alteredtarget nucleotide sequence; and (2) wherein the regenerated plantincludes in its genome two or more genetic modifications that incombination provide at least one phenotype of interest, wherein at leastone genetic modification includes the altered target nucleotide sequencein the non-epidermal plant cell.

The subject matter of this invention further includes: (IV) At least oneof the methods described above under (I), wherein the method furtherincludes the step of chromosome doubling in the non-epidermal plant cellincluding the altered target nucleotide sequence to produce a doubledhaploid cell that is homozygous for the altered target nucleotidesequence; and wherein the method optionally further includes the step ofregeneration of a doubled haploid plant from the doubled haploid cell,wherein the regenerated doubled haploid plant includes cells that arehomozygous for the altered target nucleotide sequence. The subjectmatter of this invention therefore further includes: (V) A doubledhaploid cell that is homozygous for the altered target nucleotidesequence, provided by at least one of the methods described above under(I), wherein the method further includes the step of chromosome doublingin the non-epidermal plant cell including the altered target nucleotidesequence to produce a doubled haploid cell that is homozygous for thealtered target nucleotide sequence. The subject matter of this inventiontherefore further includes: (VI) A regenerated doubled haploid plant, orseed or plant parts of the regenerated doubled haploid plant, whereinthe regenerated doubled haploid plant is provided by at least one of themethods described above under (I), wherein the method further includesthe steps of (a) chromosome doubling in the non-epidermal plant cellincluding the altered target nucleotide sequence to produce a doubledhaploid cell that is homozygous for the altered target nucleotidesequence, and (b) regeneration of a doubled haploid plant from thedoubled haploid cell, wherein the regenerated doubled haploid plantincludes cells that are homozygous for the altered target nucleotidesequence. The subject matter of this invention also further includes:(VII) A hybrid plant having at least one parent plant that is aregenerated doubled haploid plant provided according to (VI) above.

The subject matter of this invention further includes: (VIII) A methodof providing a plant having a genetic alteration, including: (a)delivery of an effector molecule to a plant cell capable of division anddifferentiation, resulting in a genetic alteration of the plant cell;wherein the plant cell is a cell in a plant or part of a plant selectedfrom the group consisting of a plant tissue, a whole plant, an intactnodal bud, a shoot apex or shoot apical meristem, a root apex or rootapical meristem, lateral meristem, intercalary meristem, a seedling, awhole seed, a halved seed or other seed fragment, an embryo, and callus;wherein the plant is a monocot or a dicot; wherein the effector moleculeis at least one selected from the group consisting of: (i) apolynucleotide selected from the group consisting of an RNA guide for anRNA-guided nuclease, a DNA encoding an RNA guide for an RNA-guidednuclease; (ii) a nuclease selected from the group consisting of anRNA-guided nuclease, an RNA-guided DNA endonuclease, a type II Casnuclease, a Cas9, a type V Cas nuclease, a Cpf1, a CasY, a CasX, a C2c1,a C2c3, an engineered nuclease, a codon-optimized nuclease, azinc-finger nuclease (ZFN), a transcription activator-like effectornuclease (TAL-effector nuclease), Argonaute, a meganuclease orengineered meganuclease; or (iii) a polynucleotide encoding one or morenucleases capable of effecting site-specific alteration of a targetnucleotide sequence; wherein delivery includes at least one treatmentselected from the group consisting of at least one treatment selectedfrom the group consisting of: direct application; soaking or imbibition;vacuum infiltration; application of negative or positive pressure;introduction into the vascular system; microinjection; application ofultrasound or vibration; application of hydrodynamic pressure, friction,cavitation or shear stress; vortexing; centrifugation; mechanical cellwall or cell membrane deformation or breakage; enzymatic cell wall orcell membrane breakage or permeabilization; abrasion; electroporation;and treatment with at least one chemical, enzymatic, or physical agent;and (b) regeneration of a plant from the plant cell, wherein the plantincludes differentiated cells or tissues having the genetic alteration;wherein the method is optionally further characterized by one or more ofthe following: (1) wherein the genetic alteration is at least onesequence alteration selected from the group consisting of insertion of anucleotide, deletion of a nucleotide, or replacement of a nucleotide;(2) wherein the genetic alteration is heritable to succeedinggenerations; and (3) wherein the plant cell is a cell in a seedling, awhole seed, a seed fragment, a mature dissected zygotic embryo, or adeveloping embryo, and wherein the regeneration of a plant from theplant cell includes growing the plant from the seedling, whole seed,seed fragment, mature dissected zygotic embryo, or developing embryo.The subject matter of this invention also further includes: (IX) A planthaving a genetic alteration produced by any of the methods describedabove under (VIII), as well as seed of such a plant, wherein the seedcontains the genetic alteration.

The subject matter of this invention further includes: (X) A method ofidentifying a nucleotide sequence associated with a phenotype ofinterest, including: (a) contacting a population of plantcells/protoplasts with a library of gRNAs or a library ofpolynucleotides encoding gRNAs and optionally with an RNA-guided DNAnuclease, whereby the genome of the cells/protoplasts is altered,culturing the population of plant cells or plant protoplasts underconditions that permit expression of the phenotype of interest,selecting the plant cells or plant protoplasts that exhibit thephenotype of interest, and identifying the nucleotide sequence oralteration of a nucleotide sequence, wherein the nucleotide sequencethus identified is associated with the phenotype; or (b) contacting apopulation of plant cells/protoplasts with a library of gRNAs or alibrary of polynucleotides encoding gRNAs and optionally with anRNA-guided DNA nuclease, whereby the genome of the cells/protoplasts isaltered, regenerating a population of plants from the population ofplant cells or plant protoplasts, growing the population of plants underconditions that permit expression of the phenotype of interest,selecting the plants that exhibit the phenotype of interest, andidentifying the nucleotide sequence or alteration of a nucleotidesequence, wherein the nucleotide sequence thus identified is associatedwith the phenotype.

The above-described subject matter is further illustrated by thenon-limiting embodiments described throughout the specification and inthe Examples that follow.

EXAMPLES Example 1

This example illustrates a method of delivering at least one effectormolecule to a plant cell wherein the plant cell is located in a plant orplant part. More specifically, this non-limiting example describesdelivery of an RNA guide for an RNA-guided nuclease (i. e., an sgRNA)and the corresponding RNA-guided nuclease (i. e., Cas9) to anon-epidermal plant cell (i. e., a cell in a soybean embryo), resultingin editing of an endogenous plant gene (i. e., phytoene desaturase, PDS)in germline cells of excised soybean embryos. This example demonstratesdelivery of polynucleotides encoding effector molecules (sgRNAs,nucleases) through multiple barriers (e. g., multiple cell layers, seedcoat, cell walls, plasma membrane) directly into soybean germline cells,resulting in a heritable alteration of the target nucleotide sequence,PDS. The methods described do not employ the common techniques ofbacterially mediated transformation (e. g., by Agrobacterium sp.) orbiolistics.

Plasmids were designed for delivery of Cas9 (Csn1) endonuclease from theStreptococcus pyogenes Type II CRISPR/Cas system and a single guide RNA(sgRNA) targeting the endogenous phytoene desaturase (PDS) in soybean,Glycine max. The sequences of these plasmids and specific elementscontained therein are described in Tables 1 and 2 below.

TABLE 1 sgRNA vector (SEQ ID NO: 1), 3079 base pairs DNA Nucleotideposition in SEQ ID NO: 1 Description Comment   1-3079 Intact plasmid SEQID NO: 1 379-395 M13 forward primer for sequencing 412-717 Glycine maxU6 promoter 717-736 Glycine max phytoene desaturase SEQ ID NO: 2targeting sequence (gRNA) 737-812 guide RNA scaffold sequence for SEQ IDNO: 3 S. pyogenes CRISPR/Cas9 system 856-874 M13 reverse primer forsequencing complement 882-898 lac repressor encoded by lacI 906-936 lacpromoter for the E. coli lac complement operon 951-972 E. colicatabolite activator protein (CAP) binding site 1260-1848high-copy-number ColE1/pMB1/ complement pBR322/pUC origin of replication(left direction) 2019-2879 CDS for bla, beta-lactamase, AmpR complement;ampicillin selection 2880-2984 bla promoter complement

The sgRNA vector having the sequence of SEQ ID NO:1 contains nucleotidesat positions 717-812 encoding a single guide RNA having the sequence ofSEQ ID NO:4, which includes both a targeting sequence (gRNA) (SEQ IDNO:2) and a guide RNA scaffold (SEQ ID NO:3); transcription of the sgRNAis driven by a Glycine max U6 promoter at nucleotide positions 412-717.The sgRNA vector also includes lac operon and ampicillin resistancesequences for convenient selection of the plasmid in bacterial cultures.

TABLE 2 endonuclease vector (SEQ ID NO: 5), 8569 base pairs DNANucleotide position in SEQ ID NO: 4 Description Comment   1-8569 Intactplasmid SEQ ID NO: 5 379-395 M13 forward primer for sequencing  419-1908Glycine max UbiL promoter 1917-6020 Cas9 (Csn1) endonuclease from theSEQ ID NO: 6 Streptococcus pyogenes type II (encodes protein CRISPR/Cassystem with sequence of SEQ ID NO: 7) 6033-6053 nuclear localizationsignal of SV40 SEQ ID NO: 8 large T antigen (encodes peptide withsequence of SEQ ID NO: 9 6065-6317 nopaline synthase (NOS) terminatorand poly(A) signal 6348-6364 M13 reverse primer for sequencingcomplement 6372-6388 lac repressor encoded by lacI 6396-6426 lacpromoter for the E. coli lac complement operon 6441-6462 E. colicatabolite activator protein (CAP) binding site 6750-7338high-copy-number ColE1/pMB1/ complement pBR322/pUC origin of replication(left direction) 7509-8369 CDS for bla, beta-lactamase, AmpR complement;ampicillin selection 8370-8474 bla promoter complement

The endonuclease vector having the sequence of SEQ ID NO:5 containsnucleotides at positions 1917-6020 having the sequence of SEQ ID NO:6and encoding the Cas9 nuclease from Streptococcus pyogenes that has theamino acid sequence of SEQ ID NO:7, and nucleotides at positions6033-6053 having the sequence of SEQ ID NO:8 and encoding the nuclearlocalization signal (NLS) of simian virus 40 (SV40) large T antigen thathas the amino acid sequence of SEQ ID NO:9. Transcription of the Cas9nuclease and adjacent SV40 nuclear localization signal is driven by aGlycine max UbiL promoter at nucleotide positions 419-1908; theresulting transcript including nucleotides at positions 1917-6053 havingthe sequence of SEQ ID NO:10 encodes a fusion protein having thesequence of SEQ ID NO:11 wherein the Cas9 nuclease is linked through a4-residue peptide linker to the SV40 nuclear localization signal. Theendonuclease vector also includes lac operon and ampicillin resistancesequences for convenient selection of the plasmid in bacterial cultures.

Similar vectors for expression of nucleases and sgRNAs are alsodescribed, e. g., in Fauser et al. (2014) Plant J., 79:348-359; anddescribed at www[dot]addgene[dot[org/crispr. It will be apparent to oneskilled in the art that analogous plasmids are easily designed to encodeother guide polynucleotide or nuclease sequences, optionally includingdifferent elements (e. g., different promoters, terminators, selectableor detectable markers, a cell-penetrating peptide, a nuclearlocalization signal, a chloroplast transit peptide, or a mitochondrialtargeting peptide, etc.), and used in a similar manner. Embodiments ofnuclease fusion proteins include fusions (with or without an optionalpeptide linking sequence) between the Cas9 nuclease from Streptococcuspyogenes that has the amino acid sequence of SEQ ID NO:7 and at leastone of the following peptide sequences: (a) GRKKRRQRRRPPQ (“HIV-1 Tat(48-60)”, SEQ ID NO:12), (b) GRKKRRQRRRPQ (“TAT”, SEQ ID NO:13), (c)YGRKKRRQRRR (“TAT (47-57)”, SEQ ID NO:14), (d) KLALKLALKALKAALKLA (“MAP(KLAL)”, SEQ ID NO:15), (e) RQIRIWFQNRRMRWRR (“Penetratin-Arg”, SEQ IDNO:16), (f) CSIPPEVKFNKPFVYLI (“antitrypsin (358-374)”, SEQ ID NO:17),(g) RRRQRRKKRGGDIMGEWGNEIFGAIAGFLG (“TAT-HA2 Fusion Peptide”, SEQ IDNO:18), (h) FVQWFSKFLGRIL-NH2 (“Temporin L, amide”, SEQ ID NO:19), (i)LLIILRRRIRKQAHAHSK (“pVEC (Cadherin-5)”, SEQ ID NO:20), (j)LGTYTQDFNKFHTFPQTAIGVGAP (“Calcitonin”, SEQ ID NO:21), (k)GAAEAAARVYDLGLRRLRQRRRLRRERVRA (“Neurturin”, SEQ ID NO:22), (1)MGLGLHLLVLAAALQGAWSQPKKKRKV (“Human P1”, SEQ ID NO:23), (m)RQIKIWFQNRRMKWKKGG (“Penetratin”, SEQ ID NO:24), poly-arginine peptidesincluding (n) RRRRRRRR (“octo-arginine”, SEQ ID NO:25) and (o) RRRRRRRRR(“nono-arginine”, SEQ ID NO:26), and (p) KKLFKKILKYLKKLFKKILKYLKKKKKKKK(“(BP100x2)-K8”, SEQ ID NO:27); these nuclease fusion proteins arespecifically claimed herein. In other embodiments, such vectors are usedto produce a guide RNA (such as one or more crRNAs or sgRNAs) or thenuclease protein; guide RNAs and nucleases can be combined to produce aspecific ribonucleoprotein complex for delivery to the plant cell; in anexample, a ribonucleoprotein including the sgRNA having the sequence ofSEQ ID NO:4 and the Cas9-NLS fusion protein having the sequence of SEQID NO:11 is produced for delivery to the plant cell. Related aspects ofthe invention thus encompass ribonucleoprotein compositions containingthe ribonucleoprotein including the sgRNA having the sequence of SEQ IDNO:4 and a Cas9 fusion protein such as the Cas9-NLS fusion proteinhaving the sequence of SEQ ID NO:11, and polynucleotide compositionscontaining one or more polynucleotides including the sequences of SEQ IDNOs: 4 or 10. The above sgRNA and nuclease vectors are delivered toplant cells using compositions and methods described in thespecification.

In a first series of experiments, the sgRNA and nuclease vectors weredelivered to non-epidermal plant cells in soybean embryos usingcombinations of delivery agents and electroporation. Mature, dry soybeanseeds (cv. Williams 82) were surface-sterilized as follows. Dry soybeanseeds were held for 4 hours in an enclosed chamber holding a beakercontaining 100 milliliters 5% sodium hypochlorite solution to which 4milliliters hydrochloric acid were freshly added. Seeds remaineddesiccated after this sterilization treatment. The sterilized seeds weresplit into 2 halves by manual application of a razor blade and theembryos manually separated from the cotyledons. Each test or controltreatment was carried out on 20 excised embryos.

Experiment 1:

A delivery solution containing the sgRNA and nuclease vectors (100nanograms per microliter of each plasmid) in 0.01% CTAB(cetyltrimethylammonium bromide, a quaternary ammonium surfactant) insterile-filtered milliQ water was prepared. Each solution was chilled to4 degrees Celsius and 500 microliters were added directly to theembryos, which were then immediately placed on ice in a vacuum chamberand subjected to a negative pressure (2×10⁻³ millibar) treatment for 15minutes. Following the chilling/negative pressure treatments, theembryos were treated with electric current using a BTX-Harvard ECM-830electroporation device set with the following parameters: 50V, 25millisecond pulse length, 75 millisecond pulse interval for 99 pulses.

Experiment 2:

conditions identical to Experiment 1, except that the initial contactingwith delivery solution and negative pressure treatments were carried outat room temperature.

Additional experiments are performed as follows:

Experiment 3:

conditions identical to Experiment 1, except that the delivery solutionis prepared without CTAB but includes 0.1% Silwet L-77™ (CAS Number27306-78-1, available from Momentive Performance Materials, Albany,N.Y). Half (10 of 20) of the embryos receiving each treatment undergoelectroporation, and the other half of the embryos do not.

Experiment 4:

conditions identical to Experiment 3, except that several deliverysolutions are prepared, where each further includes 20micrograms/milliliter of one single-walled carbon nanotube preparationselected from those with catalogue numbers 704113, 750530, 724777, and805033, all obtainable from Sigma-Aldrich, St. Louis, Mo. Half (10 of20) of the embryos receiving each treatment undergo electroporation, andthe other half of the embryos do not.

Experiment 5:

conditions identical to Experiment 3, except that the delivery solutionfurther includes 20 micrograms/milliliter oftriethoxylpropylaminosilane-functionalized silica nanoparticles(catalogue number 791334, Sigma-Aldrich, St. Louis, Mo. Half (10 of 20)of the embryos receiving each treatment undergo electroporation, and theother half of the embryos do not.

Experiment 6:

conditions identical to Experiment 3, except that the delivery solutionfurther includes 9 micrograms/milliliter branched polyethylenimine,molecular weight ˜25,000 (CAS Number 9002-98-6, catalogue number 408727,Sigma-Aldrich, St. Louis, Mo.) or 9 micrograms/milliliter branchedpolyethylenimine, molecular weight ˜800 (CAS Number 25987-06-8,catalogue number 408719, Sigma-Aldrich, St. Louis, Mo.). Half (10 of 20)of the embryos receiving each treatment undergo electroporation, and theother half of the embryos do not.

Experiment 7:

conditions identical to Experiment 3, except that the delivery solutionfurther includes 20% v/v dimethylsulfoxide (DMSO, catalogue numberD4540, Sigma-Aldrich, St. Louis, Mo.). Half (10 of 20) of the embryosreceiving each treatment undergo electroporation, and the other half ofthe embryos do not.

Experiment 8:

conditions identical to Experiment 3, except that the delivery solutionfurther contains 50 micromolar nono-arginine (RRRRRRRRR, SEQ ID NO:26).Half (10 of 20) of the embryos receiving each treatment undergoelectroporation, and the other half of the embryos do not.

Experiment 9:

conditions identical to Experiment 3, except that following the vacuumtreatment, the embryos and treatment solutions are transferred tomicrocentrifuge tubes and centrifuged 2, 5, 10, or 20 minutes at 4000×g.Half (10 of 20) of the embryos receiving each treatment undergoelectroporation, and the other half of the embryos do not.

Experiment 10:

conditions identical to Experiment 3, except that following the vacuumtreatment, the embryos and treatment solutions are transferred tomicrocentrifuge tubes and centrifuged 2, 5, 10, or 20 minutes at 4000×g.

Experiment 11:

conditions identical to Experiment 4, except that following the vacuumtreatment, the embryos and treatment solutions are transferred tomicrocentrifuge tubes and centrifuged 2, 5, 10, or 20 minutes at 4000×g.

Experiment 12:

conditions identical to Experiment 5, except that following the vacuumtreatment, the embryos and treatment solutions are transferred tomicrocentrifuge tubes and centrifuged 2, 5, 10, or 20 minutes at 4000×g.

After the delivery treatment, each treatment group of embryos is washed5 times with sterile water, transferred to a petri dish containing ½ MSsolid medium (2.165 g Murashige and Skoog medium salts, catalogue numberMSP0501, Caisson Laboratories, Smithfield, Utah), 10 grams sucrose, and8 grams Bacto agar, made up to 1.00 liter in distilled water), andplaced in a tissue culture incubator set to 25 degrees Celsius. Afterthe embryos have elongated, developed roots and true leaves haveemerged, the seedlings are transferred to soil and grown out.Modification of all endogenous PDS alleles results in a plant unable toproduce chlorophyll and having a visible bleached phenotype.Modification of a fraction of all endogenous PDS alleles results inplants still able to produce chlorophyll; plants that are heterozygousfor an altered PDS gene will are grown out to seed and the efficiency ofheritable genome modification is determined by molecular analysis of theprogeny seeds.

Example 2

This example illustrates a method of delivering polynucleotides encodingeffector molecules (sgRNAs, nucleases) to a plant cell wherein the plantcell is located in a plant or plant part. More specifically, thisnon-limiting example describes delivery of an RNA guide for anRNA-guided nuclease (i. e., an sgRNA) and the corresponding RNA-guidednuclease (i. e., Cas9) to a non-epidermal plant cell (i. e., a cell in asoybean embryo), resulting in editing of an endogenous plant gene (i.e., phytoene desaturase, PDS) in germline cells of excised soybeanembryos. The polynucleotides are delivered using combinations ofchemical agents such as cationic polymers, and physical treatments suchas use of negative pressure.

The sgRNA vector (SEQ ID NO:1) and nuclease vector (SEQ ID NO:5)described in Example 1 are used in a series of experiments. Mature, drysoybean seeds (cv. Williams 82) are surface-sterilized as follows. Drysoybean seeds are held for 4 hours in an enclosed chamber holding abeaker containing 100 milliliters 5% sodium hypochlorite solution towhich 4 milliliters hydrochloric acid are freshly added. Seeds remaineddesiccated after this sterilization treatment. The sterilized seeds aresplit into 2 halves by manual application of a razor blade and theembryos manually separated from the cotyledons. Each test and controltreatment experiment is carried out on 20 excised embryos, withtreatments carried out in 96-well plates (two embryos per well).

Solutions are prepared with branched polyethylenimine (“PEI”, CAS Number9002-98-6) in sterile-filtered milliQ water. Three molecular weights ofPEI are used: molecular weight ˜25,000 (catalogue number 408727), ˜5,000(catalogue number 764582), and ˜2,500 (catalogue number 764604) (allfrom Sigma Aldrich, St. Louis, Mo.). Four concentrations of PEI areused: 1, 5, 25, and 125 micrograms/milliliter final concentrations. ThesgRNA and nuclease vectors (final concentrations of 5micrograms/microliter of each plasmid) are added to the PEI solutions,and the mixtures incubated for 1 hour at room temperature to allowPEI/DNA complexes to form. Each solution is then chilled to 4 degreesCelsius and 500 microliters is added directly to the embryos, which arethen immediately placed on ice and vacuum infiltrated (2×10⁻³ millibar)for 2 hours with shaking at 100 rpm.

Following vacuum infiltration, the embryos are rinsed with 5% sodiumhypochlorite solution, washed 5 times with sterile water, transferred toa petri dish containing ½×MS medium (2.165 g Murashige and Skoog mediumsalts, catalogue number MSP0501, Caisson Laboratories, Smithfield,Utah), 10 grams sucrose, and 8 grams Bacto agar, made up to 1.00 literin distilled water), and placed in a tissue culture incubator set to 25degrees Celsius. After the embryos have elongated, developed roots andtrue leaves have emerged, the seedlings are transferred to soil andgrown out. Modification of all endogenous PDS alleles results in a plantunable to produce chlorophyll and having a visible bleached phenotype.Modification of a fraction of all endogenous PDS alleles results inplants still able to produce chlorophyll; plants that are heterozygousfor an altered PDS gene will are grown out to seed and the efficiency ofheritable genome modification is determined by molecular analysis of theprogeny seeds.

Example 3

This example illustrates a method of delivering polynucleotides encodingeffector molecules (sgRNAs, nucleases) to a plant cell wherein the plantcell is located in a plant or plant part. More specifically, thisnon-limiting example describes delivery of a single vector encoding bothan RNA guide for an RNA-guided nuclease (i. e., an sgRNA) and thecorresponding RNA-guided nuclease (i. e., Cas9) to a non-epidermal plantcell (i. e., a cell in a soybean embryo), resulting in editing of theendogenous phytoene desaturase (PDS) in germline cells of excisedsoybean embryos. The polynucleotides are delivered using combinations ofchemical agents such as a cell-penetrating peptide or a cationicpolymer, and physical treatments such as use of negative pressure.

A plasmid (“pCas9TPC-GmPDS”) having the nucleotide sequence of SEQ IDNO:28 was designed for delivery of Cas9 (Csn1) endonuclease from theStreptococcus pyogenes Type II CRISPR/Cas system and a single guide RNA(sgRNA) targeting the endogenous phytoene desaturase (PDS) in soybean,Glycine max. The sequences of this plasmid and specific elementscontained therein are described in Table 3 below.

TABLE 3 pCas9TPC-GmPDS vector (SEQ ID NO: 28), 14548 base pairs DNANucleotide position in SEQ ID NO: 28 Description Comment   1-14548Intact plasmid SEQ ID NO: 28 1187-1816 pVS1 StaA stability protein fromthe Pseudomonas plasmid pVS1 2250-3317 pVS1 RepA replication proteinfrom the Pseudomonas plasmid pVS1 3383-3577 pVS1 oriV origin ofreplication for the Pseudomonas plasmid pVS1 3921-4061 basis of mobilityregion from pBR322 4247-4835 high-copy-number ColE1/pMB1/ complementpBR322/pUC origin of replication (left direction) 5079-5870aminoglycoside adenylyl- complement transferase (aadA), confersresistance to spectinomycin and streptomycin 6398-6422 left borderrepeat from nopaline C58 T-DNA 6599-6620 E. coli catabolite activatorprotein (CAP) binding site 6635-6665 lac promoter for the E. coli lacoperon 6673-6689 lac repressor encoded by lacI 6697-6713 M13 reverseprimer for sequencing 6728-7699 PcUbi4-2 promoter  7714-11817 Cas9(Csn1) endonuclease from the SEQ ID NO: 6 Streptococcus pyogenes type II(encodes protein CRISPR/Cas system with sequence of SEQ ID NO: 7)11830-11850 nuclear localization signal of SV40 SEQ ID NO: 8 large Tantigen (encodes peptide with sequence of SEQ ID NO: 9 11868-12336 Pea3Aterminator 12349-12736 AtU6-26 promoter 12737-12756 Glycine max phytoenedesaturase SEQ ID NO: 2 targeting sequence (gRNA) 12757-12832 guide RNAscaffold sequence for SEQ ID NO: 3 S. pyogenes CRISPR/Cas9 system12844-12868 attB2; recombination site for complement Gateway ® BPreaction 13549-14100 Streptomyces hygroscopicus bar or pat, encodesphosphinothricin acetyltransferase, confers resistance to bialophos orphosphinothricin 14199-14215 M13 forward primer, for sequencingcomplement 14411-14435 right border repeat from nopaline C58 T-DNA

The pCas9TPC-GmPDS vector having the sequence of SEQ ID NO:28 containsnucleotides at positions 12737-12832 encoding a single guide RNA havingthe sequence of SEQ ID NO:4, which includes both a targeting sequence(gRNA) (SEQ ID NO:2) and a guide RNA scaffold (SEQ ID NO:3);transcription of the single guide RNA is driven by a AtU6-26 promoter atnucleotide positions 12349-12736. This vector further containsnucleotides at positions 7714-11817 having the sequence of SEQ ID NO:6and encoding the Cas9 nuclease from Streptococcus pyogenes that has theamino acid sequence of SEQ ID NO:7, and nucleotides at positions11830-11850 having the sequence of SEQ ID NO:8 and encoding the nuclearlocalization signal (NLS) of simian virus 40 (SV40) large T antigen thathas the amino acid sequence of SEQ ID NO:9. Transcription of the Cas9nuclease and adjacent SV40 nuclear localization signal is driven by aPcUbi4-2 promoter at nucleotide positions 6728-7699; the resultingtranscript including nucleotides at positions 7714-11850 having thesequence of SEQ ID NO:10 encodes a fusion protein having the sequence ofSEQ ID NO:11 wherein the Cas9 nuclease is linked through a 4-residuepeptide linker to the SV40 nuclear localization signal. ThepCas9TPC-GmPDS vector also includes lac operon, aminoglycosideadenylyltransferase, and phosphinothricin acetyltransferase sequencesfor convenient selection of the plasmid in bacterial or plant cultures.

In a series of experiments, the pCas9TPC-GmPDS vector (SEQ ID NO:28) wasdelivered to non-epidermal plant cells in soybean embryos usingcombinations of delivery agents and application of negative pressure.Mature, dry soybean seeds (cv. Williams 82) were surface-sterilized asfollows. Dry soybean seeds were held for 4 hours in an enclosed chamberholding a beaker containing 100 milliliters 5% sodium hypochloritesolution to which 4 milliliters hydrochloric acid were freshly added.Seeds remained desiccated after this sterilization treatment. Thesterilized seeds were split into 2 halves by manual application of arazor blade and the embryos manually separated from the cotyledons. Eachtest or control treatment experiment was carried out on 10 dry excisedembryos. The excised embryos were transferred to 1.5-microlitermicrocentrifuge tubes.

Treatments included use of delivery agents including a cell-penetratingpeptide (“CPP”) having the amino acid sequenceKKLFKKILKYLKKLFKKILKYLKKKKKKKK (“(BP100x2)-K8”, SEQ ID NO:27), and acationic polymer, branched polyethylenimine (“PEI”), molecular weight˜25,000 (CAS Number 9002-98-6, catalogue number 408727, Sigma-Aldrich,St. Louis, Mo.). Stock solutions of the pCas9TPC-GmPDS vector (SEQ IDNO:28) (500 nanograms/microliter), CPP (10 micrograms/microliter), andPEI (10 micrograms/microliter) were prepared. Treatment solutions wereprepared according to Table 4 and incubated 1 hour at room temperatureto allow the plasmid to form complexes with the CPP or PEI deliveryagents. Control treatment solutions included sterile milliQ water (noplasmid, no delivery agents) as well as a solution of the plasmid inmilliQ water with no delivery agents.

TABLE 4 Cell-penetrating Plasmid peptide (SEQ ID NO: 28), (SEQ ID NO:27), Branched PEI, micrograms/ micrograms/ micrograms/ Treatmentmilliliter milliliter milliliter CPP-1 20 1 0 CPP-2 20 10 0 CPP-3 20 5000 CPP-4 1 500 0 PEI-1 5 0 50 PEI-2 5 0 75 PEI-3 5 0 100 PEI-4 5 0 250

Each tube received 1000 microliters of the prepared treatment solutionsand placed on ice. The tubes were vacuum infiltrated (2×10⁻³ millibar)for 2 hours in a desiccator submerged in ice. Following vacuuminfiltration, the embryos were rinsed with 5% sodium hypochloritesolution, washed 5 times with sterile water, transferred to a petri dishcontaining ½×MS medium (2.165 g Murashige and Skoog medium salts,catalogue number MSP0501, Caisson Laboratories, Smithfield, Utah), 10grams sucrose, and 8 grams Bacto agar, made up to 1.00 liter indistilled water), and placed in a tissue culture incubator set to 25degrees Celsius. After the embryos have elongated, developed roots andtrue leaves have emerged, the seedlings are transferred to soil andgrown out to seed. Modification of all endogenous PDS alleles results ina plant unable to produce chlorophyll and having a visible bleachedphenotype. Modification of a fraction of all endogenous PDS allelesresults in plants still able to produce chlorophyll; plants that areheterozygous for an altered PDS gene will are grown out to seed and theefficiency of heritable genome modification is determined by molecularanalysis of the progeny seeds.

Example 4

This example illustrates a method of delivering at least one effectormolecule to a plant cell wherein the plant cell is located in a plant orplant part. More specifically, this non-limiting example illustrates amethod of delivering a polynucleotide composition including a guide RNA(gRNA) to a non-epidermal plant cell in a seed of a plant and editing ofan endogenous plant gene (phytoene desaturase, PDS) in germline cells ofNicotiana benthamiana seeds. This example demonstrates delivery ofpolynucleotides encoding effector molecules (sgRNAs, nucleases) throughmultiple barriers (e. g., multiple cell layers, seed coat, cell walls,plasma membrane) directly into Nicotiana benthamiana germline cells,resulting in a heritable alteration of the target nucleotide sequence,PDS. The methods described do not employ the common techniques ofbacterially mediated transformation (e. g., by Agrobacterium sp.) orbiolistics.

A plasmid (“pCas9TPC-NbPDS”) having the nucleotide sequence of SEQ IDNO:29 was designed for delivery of Cas9 (Csn1) endonuclease from theStreptococcus pyogenes Type II CRISPR/Cas system and a single guide RNA(sgRNA) targeting the endogenous phytoene desaturase (PDS) in Nicotianabenthamiana; see Nekrasov et al. (2013) Nature Biotechnol., 31:691-693.The sequences of this plasmid and specific elements contained thereinare described in Table 5 below.

TABLE 5 pCas9TPC-NbPDS vector (SEQ ID NO: 29), 14548 base pairs DNANucleotide position in SEQ ID NO: 29 Description Comment   1-14548Intact plasmid SEQ ID NO: 29 1187-1816 pVS1 StaA stability protein fromthe Pseudomonas plasmid pVS1 2250-3317 pVS1 RepA replication proteinfrom the Pseudomonas plasmid pVS1 3383-3577 pVS1 oriV origin ofreplication for the Pseudomonas plasmid pVS1 3921-4061 basis of mobilityregion from pBR322 4247-4835 high-copy-number ColE1/pMB1/ ComplementpBR322/pUC origin of replication (left direction) 5079-5870aminoglycoside adenylyl- Complement transferase (aadA), confersresistance to spectinomycin and streptomycin 6398-6422 left borderrepeat from nopaline C58 T-DNA 6599-6620 E. coli catabolite activatorprotein (CAP) binding site 6635-6665 lac promoter for the E. coli lacoperon 6673-6689 lac repressor encoded by lacI 6697-6713 M13 reverseprimer for sequencing 6728-7699 PcUbi4-2 promoter  7714-11817 Cas9(Csn1) endonuclease from the SEQ ID NO: 6 Streptococcus pyogenes type II(encodes protein CRISPR/Cas system with sequence of SEQ ID NO: 7)11830-11850 nuclear localization signal of SV40 SEQ ID NO: 8 large Tantigen (encodes peptide with sequence of SEQ ID NO: 9 11868-12336 Pea3Aterminator 12349-12736 AtU6-26 promoter 12737-12756 Nicotianabenthamiana phytoene SEQ ID NO: 30 desaturase targeting sequence12757-12832 guide RNA scaffold sequence for SEQ ID NO: 3 S. pyogenesCRISPR/Cas9 system 12844-12868 attB2; recombination site for ComplementGateway ® BP reaction 13549-14100 Streptomyces hygroscopicus bar or pat,encodes phosphinothricin acetyltransferase, confers resistance tobialophos or phosphinothricin 14199-14215 M13 forward primer, forsequencing Complement 14411-14435 right border repeat from nopaline C58T-DNA

The pCas9TPC-NbPDS vector having the sequence of SEQ ID NO:29 containsnucleotides at positions 12737-12832 encoding a single guide RNA havingthe sequence of SEQ ID NO:31, which includes both a targeting sequence(gRNA) (SEQ ID NO:30) and a guide RNA scaffold (SEQ ID NO:3);transcription of the single guide RNA is driven by a AtU6-26 promoter atnucleotide positions 12349-12736. This vector further containsnucleotides at positions 7714-11817 having the sequence of SEQ ID NO:6and encoding the Cas9 nuclease from Streptococcus pyogenes that has theamino acid sequence of SEQ ID NO:7, and nucleotides at positions11830-11850 having the sequence of SEQ ID NO:8 and encoding the nuclearlocalization signal (NLS) of simian virus 40 (SV40) large T antigen thathas the amino acid sequence of SEQ ID NO:9. Transcription of the Cas9nuclease and adjacent SV40 nuclear localization signal is driven by aPcUbi4-2 promoter at nucleotide positions 6728-7699; the resultingtranscript including nucleotides at positions 7714-11850 having thesequence of SEQ ID NO:10 encodes a fusion protein having the sequence ofSEQ ID NO:11 wherein the Cas9 nuclease is linked through a 4-residuepeptide linker to the SV40 nuclear localization signal. ThepCas9TPC-NbPDS vector also includes lac operon, aminoglycosideadenylyltransferase, and phosphinothricin acetyltransferase sequencesfor convenient selection of the plasmid in bacterial or plant cultures.

In a series of experiments, the pCas9TPC-NbPDS (SEQ ID NO:29) wasdelivered to non-epidermal plant cells in Nicotiana benthamiana intactseeds using combinations of delivery agents and physical techniques.Mature, dry N. benthamiana seeds were surface-sterilized as follows. DryN. benthamiana seeds were held for 3 hours in an enclosed chamberholding a beaker containing 100 milliliters 5% sodium hypochloritesolution to which 4 milliliters hydrochloric acid were freshly added.Seeds remained desiccated after this sterilization treatment. Each testor control treatment experiment was carried out on 10 sterilized seeds.The following treatments were performed:

Treatment 1 (vacuum control): Seeds were pre-incubated in 400microliters Tris-EDTA (TE) buffer on ice for 3 hours under vacuum,followed by an overnight incubation at 4 degrees Celsius and then arecovery period of 7 hours at room temperature. The TE buffer wasremoved by aspiration and the seeds resuspended in 400 microliters of50% glycerol in milliQ water. Seeds were plated on ½ MS solid media (seeExample 1) and germination scored.

Treatment 2 (vacuum/electroporation control): identical to treatment 1,except that after removal of the TE buffer, the seeds were resuspendedin 400 or 800 microliters of 50% glycerol in milliQ water, transferredrespectively to a 2 or 4 millimeter gap cuvette, and subjected toelectroporation using a BTX-Harvard ECM-830 electroporation device setwith the following parameters: 100V, 25 millisecond pulse length, 75millisecond pulse interval for 99 pulses, followed by 400V, 99millisecond pulse length, 297 millisecond pulse interval for 5 pulses.The seeds were then plated on ½ MS solid media (see Example 1) andgermination scored.

Treatment 3 (vacuum/DNA): identical to treatment 1, except that seedswere incubated in a solution of 1 microgram of the pCas9TPC-NbPDS (SEQID NO:29) DNA in 200 microliters TE buffer.

Treatment 4: (vacuum/electroporation/DNA): identical to treatment 2,except that seeds were incubated in a solution of 1 microgram of thepCas9TPC-NbPDS (SEQ ID NO:29) DNA in 200 microliters TE buffer, and theelectroporation solution further includes 5 nanograms/microliter of thepCas9TPC-NbPDS (SEQ ID NO:29) DNA.

Modification of all endogenous PDS alleles results in a plant unable toproduce chlorophyll and having a visible bleached phenotype.Modification of a fraction of all endogenous PDS alleles results inplants still able to produce chlorophyll; plants that are heterozygousfor an altered PDS gene will are grown out to seed and the efficiency ofheritable genome modification is determined by molecular analysis of theprogeny seeds.

Example 5

This example illustrates a method of delivering at least one effectormolecule to a plant cell wherein the plant cell is located in a plant orplant part. More specifically, this non-limiting example illustrates amethod of delivering a polynucleotide composition including a guide RNA(gRNA) to a non-epidermal plant cell in a seed of a plant and editing ofan endogenous plant gene (alcohol dehydrogenase, ADH1, NCBI locus tagZEAMMB73_889219, with the sequence of SEQ ID NO:32) in germline cells ofmaize (Zea mays) seeds. This example demonstrates delivery of effectormolecules including polynucleotides (multiple crRNA:tracrRNAcombinations) and an RNA-guided nuclease in the form of aribonucleoprotein complex, through multiple barriers (e. g., multiplecell layers, seed coat, cell walls, plasma membrane) directly into Zeamays germline cells, resulting in a selectable, heritable alteration ofthe target nucleotide sequence, ADH1, thus conferring resistance toallyl alcohol. The methods described do not employ the common techniquesof bacterially mediated transformation (e. g., by Agrobacterium sp.) orbiolistics.

Three individual crRNAs (Alt-R™) including the guide RNA (gRNA)sequences GGCAAGCCACTGTCGATCG (SEQ ID NO:33), GGCCTCCCAGAAGTAGACGT (SEQID NO:34), and ACGCGCACCTCCATGGCCTG (SEQ ID NO:35) were synthesized byIDT (Coralville, Iowa). Individual crRNA:tracrRNA duplex solutions areprepared by combining equimolar amounts of a single crRNA with atracrRNA synthesized by IDT (Coralville, Iowa) to a final concentrationof 100 micromolar; each crRNA/tracrRNA mixture is heated to 95 degreesCelsius for 5 minutes and then allowed to cool to room temperature toform the crRNA:tracrRNA duplex solutions. Ribonucleoprotein (RNP)solutions are prepared by combining equimolar amounts of eachcrRNA:tracrRNA duplex and a purified Cas9 fusion protein having anuclear localization signal (NLS) on either terminus (sNLS-spCas9-sNLS,purchased from Aldevron, Fargo, N. Dak.) to a final concentration of 100micromolar and incubating the mixtures at room temperature for 5 minutesto allow the ribonucleoprotein complexes to form.

Mature, dry kernels (seeds) of B73 maize are surface-sterilized asfollows. Dry maize kernels are held for 4 hours in an enclosed chamberholding a beaker containing 100 milliliters 5% sodium hypochloritesolution to which 4 milliliters hydrochloric acid are freshly added. Thekernels remain desiccated after this sterilization treatment. Embryosare manually separated from the cotyledons and endosperm using a scalpelblade. Each test or control treatment experiment is carried out on 10dry excised embryos. The excised embryos are transferred to1.5-microliter microcentrifuge tubes.

To each microfuge tube is added 180 microliters of maize washingsolution (0.6 molar D-mannitol, 4 millimolar2-(N-morpholino)ethanesulfonic acid (MES) buffer, pH 5.7, 20 millimolarKCl) and 20 microliters of the RNP solution. The microcentrifuge tubesare tapped gently to mix and immediately placed on ice and vacuuminfiltrated (2×10⁻³ millibar) for 2 hours with shaking at 100 rpm.Following vacuum infiltration, the embryos are rinsed with 5% sodiumhypochlorite solution, washed 5 times with sterile water, transferred toa petri dish containing ½×MS medium (2.165 g Murashige and Skoog mediumsalts, catalogue number MSP0501, Caisson Laboratories, Smithfield,Utah), 10 grams sucrose, and 8 grams Bacto agar, made up to 1.00 literin distilled water), and placed in a tissue culture incubator set to 25degrees Celsius. After the embryos have elongated, developed roots andtrue leaves have emerged, the seedlings are treated with 5 or 20micromolar allyl alcohol for 24 hours. The seedlings are then washed 5times with sterile water, transferred to soil and grown out.Modification of the endogenous ADH1 results in a plant having anobservable phenotype, i. e., resistance to allyl alcohol-inducedtoxicity. Surviving maize seedlings are grown out to seed and theefficiency of heritable genome modification is determined by molecularanalysis of the progeny seeds.

Example 6

This example illustrates a method of delivering at least one effectormolecule to a plant cell wherein the plant cell is located in a plant orplant part. More specifically, this non-limiting example illustrates amethod of delivering a polynucleotide composition including at least onecrRNA or gRNA or sgRNA to a non-epidermal plant cell in a seed of aplant, resulting in editing of at least one endogenous plant gene. Thisexample demonstrates direct delivery by microinjection of effectormolecules (e. g., at least one crRNA or sgRNA or a polynucleotideencoding at least one crRNA or sgRNA or an RNA-guided nuclease or apolynucleotide that encodes the RNA-guided nuclease) directly into maize(Zea mays) zygotes; the embryos are isolated and allowed to shoot, andthe resulting maize plants containing the desired genomic edit oralteration of the target nucleotide sequence are subsequentlyidentified. The methods described do not employ the common techniques ofbacterially mediated transformation (e. g., by Agrobacterium sp.) orbiolistics.

A non-limiting example of a microinjection protocol utilized maize B73fertilized cobs (ears) (collected 1 day after pollination). All steps ofthis protocol were performed under a laminal flow hood. Husks and silkswere removed from the cobs. The cobs were transversely cut intoapproximately 3-centimeter segments with the top and bottom twocentimeters of each cob discarded. The segments were surface-sterilizedfor 10 minutes in 70% ethanol followed by three washes in distilled,autoclaved water of one minute each.

Ethanol-sterilized fifty-milliliter tube caps were used as specimenmounting blocks, to which two pairs of ovaries cut from the prepared cobslices were glued with a thin layer of fast-facing adhesive (e. g.,Loctite Control Gel Premium Super Glue); one pair of ovaries was mountedfacing the other pair's basal ends. The mounted ovaries were attached toa modified specimen tray of a Vibratome (PELCO easiSlicer™, Ted Pella,Inc.) with the stylar ends facing the blade. Ovaries were sectioned at220 micrometers from the ovarian surface. Sections that contained embryosacs were collected for microinjection on MMIM (modified maize inductionmedium). To prepare MMIM, 2.2 g Murashige and Skoog (MS) medium, 50 gsucrose, 10 g mannitol, and 2.5 g Phytagel were dissolved in 500milliliters water and pH adjusted to 5.8; after autoclaving, indoleacetic acid or 1-naphthaleneacetic acid (0.1 milligrams/liter finalconcentration), 6-benzylaminopurine (0.5 milligrams/liter finalconcentration), and vitamins (1× final concentration) are added.

The target gene selected for editing was the maize (Zea mays) alcoholdehydrogenase ADH1 (seewww[dot]maizegdb[dot]org/gene_centedgene/GRMZM2G442658) with the partialgenomic sequence:

(SEQ ID NO: 36) GAACAGTGCCGCAGTGGCGCTGATCTTGTATGCTATCCTGCAATCGTGGTGAACTTATTTCTTTTATATCCTTTACTCCCATGAAAAGGCTAGTAATCTTTCTCGATGTAACATCGTCCAGCACTGCTATTACCGTGTGGTCCATCCGACAGTCTGGCTGAACACATCATACGATCTATGGAGCAAAAATCTATCTTCCCTGTTCTTTAATGAAGGACGTCATTTTCATTAGTATGATCTAGGAATGTTGCAACTTGCAAGGAGGCGTTTCTTTCTTTGAATTTAACTAACTCGTTGAGTGGCCCTGTTTCTCGGACGTAAGGCCTTTGCTGCTCCACACATGTCCATTCGAATTTTACCGTGTTTAGCAAGGGCGAAAAGTTTGCATCTTGATGATTTA GCTTGACT ATGCGATTGCTTTCCTGGACCCGTGCAGCTGCGGTGGCATGGGAGGCCGGCAAGCCACTGTCGATCGAGGAGGTGGAGGTAGCGCCTCCGCAGGCCATGGAGGTGCGCGTCAAGATCCTCTTCACCTCGCTCTGCCACACCG ACGTCTACTTCTGGGAGGCCA AGGTATCTAATCAGCCATCCCATTTGTGATCTTTGTCAGTAGATATGATACAACAACTCGCGGTTGACTTGCGCCTTCTTGGCGGCTTATCTGTCTTAGGGGCAGACTCCCGTGTTCCCTCGGATCTTT GGCCACGAGGCTGGAGGGTA;the first exon (SEQ ID NO:37), located at nucleotide positions 409-571of SEQ ID NO:36 is indicated by bold, underlined text and guide RNA(crRNA) sequences were designed to edit this exon.

A ribonucleoprotein (RNP) was prepared with Cas9 nuclease (Aldevron,Fargo, N. Dak.) and a guide RNA complex of a crRNA (ZmADH1-B) having thesequence GGCCUCCCAGAAGUAGACGUGUUUUAGAGCUAUGCU (SEQ ID NO:38) and atracrRNA (both purchased from Integrated DNA Technologies, Coralville,Iowa). A guide RNA (gRNA) complex was prepared as follows: 30microliters of 100 micromolar crRNA were mixed with 30 microliters of100 micromolar tracrRNA, heated at 95 degrees Celsius for 5 minutes, andthen cooled to room temperature. To the cooled gRNA solution, 100micrograms Cas9 nuclease (Aldevron, Fargo, N. Dak.) was added and themixture incubated 5 minutes at room temperature to allow theribonucleoprotein (RNP) complex to form. A microinjection mixturecontaining the RNP complex was prepared by taking a volume (e. g., 30microliters) of the RNP solution and adding sufficient 10×Cas9 reactionbuffer (20 millimolar HEPES, 1 molar NaCl, 50 millimolar MgCl2, 1millimolar EDTA) to yield a 1× buffer concentration in the finalmixture. The microinjection mixture was centrifuged through a Milliporefilter (UFC30VV25) at 13,000 rpm for 10 minutes at room temperature.

For microinjection of the maize zygotes, 2.5 microliters of the filteredinjection mix were loaded into a borosilicate needle (catalogue numberG100E-4, Warner Instruments, Hamden, Conn.), previously pulled with aP1000 micropipette puller (Sutter Instrument, Novato, Calif.) with thefollowing settings: Heat: Ramp-20; Pull: 140; Velocity: 70; Delay: 200;Pressure: 510; Ramp: 499. The needle was opened with a micropipettebeveller (BV-10, Sutter Instrument, Novato, Calif.) with an angle of 35degrees. The egg apparatus was visualized with basal illumination with afluorescence stereoscope (model SMZ18, Nikon, Tokyo, Japan). Theinjection mix was injected into the egg apparatus using a FemtoJet 4iwith a PatchMan micromanipulator (both from Eppendorf, Hauppauge, N.Y.).Embryo sacs were recovered in MMIM medium. The embryos were kept in thedark at 26 degrees Celsius until shoots formed, and then kept in lightat 26 degrees Celsius. Shoots thus produced are optionally grown underculture conditions including exposure to low concentrations (e. g., 5 or20 micromolar) of allyl alcohol (which is converted by a functional ADH1to acrolein, which is toxic to the cell), thus permitting selection byexpression of the predicted phenotype, i. e., decreased allyl alcoholsusceptibility in shoots or plants wherein one or both copies of theendogenous ADH1 gene has been disrupted. Surviving maize seedlings aregrown out to seed and the efficiency of heritable genome modification isdetermined by molecular analysis of the progeny seeds.

One of skill in the art would recognize that there are alternativereagents and compositions including such reagents that are useful forintroducing alterations or edits into the genome (e. g., use of CRISPRnucleases other than Cas9, such as CasX, CasY, and Cpf1, zinc-fingernucleases (ZFNs), transcription activator-like effector nucleases(TAL-effector nucleases or TALENs), Argonaute proteins, or ameganuclease or engineered meganuclease) and thus similar embodiments ofthe microinjection technique described herein include use of any ofthese reagents. Similarly, the microinjection technique described hereinis generally applicable to any plant cell of sufficient size to permitmicroinjection (e. g., germline cells or cells that develop intogermline cells, egg cells, zygote cells, embryo cells, meristematiccells), and of any plant species (e. g., alfalfa (Medicago sativa),almonds (Prunus dulcis), apples (Malus x domestica), apricots (Prunusarmeniaca, P. brigantine, P. mandshurica, P. mume, P. sibirica),asparagus (Asparagus officinalis), bananas (Musa spp.), barley (Hordeumvulgare), beans (Phaseolus spp.), blueberries and cranberries (Vacciniumspp.), cacao (Theobroma cacao), canola and rapeseed or oilseed rape,(Brassica napus), carnation (Dianthus caryophyllus), carrots (Daucuscarota sativus), cassava (Manihot esculentum), cherry (Prunus avium),chickpea (Cider arietinum), chicory (Cichorium intybus), chili peppersand other capsicum peppers (Capsicum annuum, C. frutescens, C. chinense,C. pubescens, C. baccatum), chrysanthemums (Chrysanthemum spp.), coconut(Cocos nucifera), coffee (Coffea spp. including Coffea arabica andCoffea canephora), cotton (Gossypium hirsutum L.), cowpea (Vignaunguiculata), cucumber (Cucumis sativus), currants and gooseberries(Ribes spp.), eggplant or aubergine (Solanum melongena), eucalyptus(Eucalyptus spp.), flax (Linum usitatissumum L.), geraniums (Pelargoniumspp.), grapefruit (Citrus x paradisi), grapes (Vitus spp.) includingwine grapes (Vitus vinifera), guava (Psidium guajava), irises (Irisspp.), lemon (Citrus limon), lettuce (Lactuca sativa), limes (Citrusspp.), maize (Zea mays L.), mango (Mangifera indica), mangosteen(Garcinia mangostana), melon (Cucumis melo), millets (Setaria spp,Echinochloa spp, Eleusine spp, Panicum spp., Pennisetum spp.), oats(Avena sativa), oil palm (Ellis quineensis), olive (Olea europaea),onion (Allium cepa), orange (Citrus sinensis), papaya (Carica papaya),peaches and nectarines (Prunus persica), pear (Pyrus spp.), pea (Pisasativum), peanut (Arachis hypogaea), peonies (Paeonia spp.), petunias(Petunia spp.), pineapple (Ananas comosus), plantains (Musa spp.), plum(Prunus domestica), poinsettia (Euphorbia pulcherrima), Polish canola(Brassica rapa), poplar (Populus spp.), potato (Solanum tuberosum),pumpkin (Cucurbita pepo), rice (Oryza sativa L.), roses (Rosa spp.),rubber (Hevea brasiliensis), rye (Secale cereale), safflower (Carthamustinctorius L), sesame seed (Sesame indium), sorghum (Sorghum bicolor),soybean (Glycine max L.), squash (Cucurbita pepo), strawberries(Fragaria spp., Fragaria x ananassa), sugar beet (Beta vulgaris),sugarcanes (Saccharum spp.), sunflower (Helianthus annus), sweet potato(Ipomoea batatas), tangerine (Citrus tangerina), tea (Camelliasinensis), tobacco (Nicotiana tabacum L.), tomato (Lycopersiconesculentum), tulips (Tulipa spp.), turnip (Brassica rapa rapa), walnuts(Juglans spp. L.), watermelon (Citrulus lanatus), wheat (Tritiumaestivum), and yams (Discorea spp.)). Non-limiting embodiments includemicroinjection delivery of DNA or RNP editing reagents to egg cells,zygote cells, embryo cells, and meristematic cells of maize, rice,wheat, barley, rye, millet, sorghum, soybean, cotton, brassicas(including oilseed brassicas and sugar beet), solanaceous plants(including tomato, pepper, potato, and eggplant), strawberry, banana,plantain, citrus fruits, coffee, cacao, and sugarcanes.

Example 7

This example illustrates a method of delivering at least one effectormolecule to a plant cell wherein the plant cell is located in a plant orplant part. More specifically, this non-limiting example illustrates amethod of delivering a polynucleotide composition including at least onecrRNA or gRNA or sgRNA to non-epidermal plant cells, resulting inediting of at least one endogenous plant gene. This example demonstratesdirect delivery of effector molecules (e. g., at least one crRNA orsgRNA or a polynucleotide encoding at least one crRNA or sgRNA or anRNA-guided nuclease or a polynucleotide that encodes the RNA-guidednuclease) by gold microparticle bombardment directly into germline cellsof excised soybean (Glycine max) embryos.

The target genes selected for editing were two endogenous soybean(Glycine max) phytoene desaturase (PDS) genes, Glyma.11g239000 andGlyma.18g003900 (see, e. g.,www[dot]soybase[dot]org/sbt/search/search_results.php?category=FeatureName&version=Glyma2[dot]0&s earch_term=Glyma[dot]18g003900). The first PDS gene,Glyma.11g239000 has the genomic sequence of SEQ ID NO:39. The second PDSgene, Glyma.18g003900, has the genomic sequence of SEQ ID NO:40.

Four guide RNA (gRNA) sequences were designed to cleave both soybean PDSgenes, Glyma.11g253000 (SEQ ID NO:39) and Glyma18g003900 (SEQ ID NO:40):GmPDS gRNA.1 GAAGCAAGAGACGUUCUAGG (SEQ ID NO:41), GmPDS gRNA.2GGUUGCUGCAUGGAAAGACA (SEQ ID NO:42), GmPDS gRNA.3 CCAUAUGUUGAGGCUCAAGA(SEQ ID NO:43), and GmPDS gRNA.4 GAUCAUAUUCAGUCCUUGGG (SEQ ID NO:44).These were provided as single guide RNAs (sgRNAs), chimeric RNAs, eachof which included one of the gRNA sequences and a guide RNA scaffoldsequence (SEQ ID NO:3). All four gRNA sequences had been previouslyvalidated by an in vitro Cas9 assay and were shown to be capable ofcleaving both soybean phytoene desaturase genes. The first PDS gene,Glyma.11g239000 (SEQ ID NO:39) is cleaved between nucleotide positions2379-2340, 2653-2654, 3931-3932, and 4795-4796. The second PDS gene,Glyma.18g003900, (SEQ ID NO:40) is cleaved between nucleotide positions2217-2218, 2490-2491, 5370-5371, and 6130-6131.

In a first series of experiments, the sgRNA and nuclease vectors weredelivered by gold microparticle bombardment to non-epidermal cells insoybean embryonic axes. Mature, dry soybean seeds (cv. Williams 82) weresurface-sterilized by holding overnight in an enclosed chamber holding abeaker containing 100 milliliters 5% sodium hypochlorite solution towhich 4 milliliters hydrochloric acid were freshly added. The sterilizedseeds were imbibed in sterile water for 2-20 hours. Seeds were dividedby inserting a razor blade into the hilum leaving the embryonic axesintact. The pericarp was removed and the tip of the radicle excised. Theleaf primordia and a thin layer of the shoot apical meristems wereexcised with a scalpel with the aid of a dissecting microscope. Preparedexplants were placed on pre-bombardment medium (“Recipe X” with theaddition of 2 milligrams/liter 6-benzylaminopurine) for 2-3 days in thedark at 26 (plus or minus 2) degrees Celsius. In an alternativeprotocol, explants were placed on osmoticum medium (“Recipe X” modifiedby the addition of 36.8 grams/liter sorbitol and 36.8 grams/litermannitol) for four hours prior to bombardment. To make a 1-literquantity of “Recipe X” medium, mix 4.43 g MS salts with B5 vitamins, 10milliliter 0.2 molar MES hydrate stock solution, 100 milligramsmyo-inositol, 30 grams sucrose, 8 grams Oxoid agar (Remel, Inc. Lenexa,Kans.) and bring volume to 1 liter with water. Adjust pH to 5.8 beforeadding agar and autoclaving. Add 6-benzylaminopurine (BA) after coolingto about 50 degrees Celsius.

Gold microparticles were prepared as follows. In the followingnon-limiting experiments, 1.0 micrometer gold microparticles were used(Bio-Rad, Hercules, Calif.). In other protocols, gold microparticles ofother sizes (e. g., 0.6 or 1.6 micrometer) are also useful gold.Approximately 15-20 milligrams of gold microparticles were transferredto sterile 1.5 milliliter microcentrifuge tubes. Cold absolute ethanol(500 microliters) was added to each tube, and the tubes were placed inthe ultrasonicating water bath for 15 seconds. Gold microparticles wereallowed to settle ˜10-30 minutes followed by pelleting by centrifugationfor 1 minute at 3000 rpm. The supernatant was removed and the pellet wascarefully rinsed with 1 milliliter ice-cold sterile water. The tubeswere tapped gently to disturb the pellets, which were then allowed tosettle again. The rinse step was repeated two more times. After thethird rinse, the microparticles were pelleted 15 seconds at 5000 rpm,and the final supernatant removed. The pellet was resuspended in 500microliters sterile water to form a “1×” concentration, placed in theultrasonicating water bath for 15 seconds, and immediately after wasvortexed. Aliquots of 50 microliters were transferred to 1.5-millilitermicrocentrifuge tubes, with the original preparation continuallyvortexed during the transfers. The 1× aliquots were stored at −20degrees Celsius.

Prior to precipitation of DNA on gold microparticles, soy explants areembedded in pre-bombardment medium with the shoot apical meristemarranged parallel with the medium's surface and directly facing thetrajectory of the DNA coated microparticles. Approximately, 20-40explants were placed in the center of the plate, corresponding to the˜3.5-centimeter diameter circle of the tissue platform (Bio-Rad,Hercules, Calif.). A tube of 1× prepared gold was used for bombardmentof three media plates of soy explants. Prepared 1× tubes were thawed onice, placed in the ultrasonicating water bath for 15 seconds, and thencentrifuged at 2000 rpm for 2 minutes. The supernatant was removed andthe gold microparticles were resuspended in either 25 microliters DNA (1microgram/microliter) solution or 25 microliters sterile water as acontrol. The following was added in order, vortexing between eachaddition: 220 microliters sterile water, 250 microliters 2.5 molarcalcium chloride, and 50 microliters 0.1 molar spermidine. The tubeswere placed on ice for 5 minutes, vortexed for ˜2 minutes at roomtemperature, and then centrifuged at 500 rpm for 5 minutes. Thesupernatant was removed and the pellet was resuspended in 600microliters absolute ethanol. The tubes were centrifuged for 1 minute at14K rpm. The supernatant was removed and the pellet was resuspended in36 microliters absolute ethanol. (To conserve the amount of gold used,the pellet can be resuspended in about 90 microliters absolute ethanol,and about 10 microliters or about 444 nanograms gold used for each shotfor 9 shots.) DNA-coated gold (11 microliters) was placed in the centerof autoclaved macrocarriers (Bio-Rad, Hercules, Calif.) and allowed todry for approximately 5-10 minutes. The PDS-1000/He Biolistic® particledelivery system (Bio-Rad, Hercules, Calif.) was assembled. The rupturediscs (1,100 psi rupture discs, Bio-Rad, Hercules, Calif.; 900 or 650psi rupture discs can also be used) were dipped in 70% ethanol tosterilize, placed in the retaining cap, and tightened with themanufacturer's supplied wrench. The autoclaved stopping screen wasplaced in the macrocarrier assembly followed by the DNA-coated goldmacrocarrier. The system was assembled as directed in the manual. Thedistance used from stopping screen to soy explants was 6 centimeters.The gun was fired when the vacuum in the chamber reached 27-28 inches ofHg.

After bombardment, explants were transferred to Recipe X mediumcontaining 0.5 milligrams/liter 6-benzylaminopurine. Plates withbombarded explants were placed in the dark for 2-4 days at 26 (plus orminus 2) degrees Celsius, then moved to a 16-hour light (75micromoles)/8-hour dark light regime at 26 (plus or minus 2) degreesCelsius for several days to weeks depending on assay performed. Fornon-destructive assays, soybean shoots were sampled and explants movedto fresh Recipe X medium containing 0.5 milligrams/liter6-benzylaminopurine. When shoots reached about 2-3 centimeters inlength, explants where transferred to shoot elongation media (“RecipeY”). To make 1 liter of “Recipe Y” medium, mix 4.43 grams MS salts withB5 vitamins, 0.59 grams MES hydrate, and 30 grams sucrose in 1 literwater, adjust pH to 5.7, and add 3 grams Phytagel. Autoclave 35 minuteson liquid cycle and cool to 50 degrees Celsius. In a laminar flow hood,add to 1 liter of cooled medium 0.5 milligrams gibberellic acid (as apremade stock, G362, PhytoTechnologies Laboratories, Shawnee Mission,Kans.), 500 microliters 50 milligrams/milliliter asparagine stocksolution, 5 milligrams glutamine, 400 microliters indole acetic acid (asa 1 milligram/milliliter stock), and 1 milligram trans-zeatin riboside.Pour 100 milliliters per phytatray and allow to cool; store at roomtemperature. After approximately two weeks of shoot elongation, shootswere of sufficient size to transfer to Jiffy peat pellets, and werelater transplanted to soilless mix in pots for maturation. Modificationof the endogenous PDS gene(s) results in a plant having an observablebleached phenotype.

In another series of experiments, ribonucleoprotein (RNP) including aCas9 nuclease and a guide RNA (gRNA) complex (crRNA-tracrRNA complex)was used for delivery of soybean phytoene desaturase guide RNAs to shootapical meristem cells via gold microparticle bombardment. The RNP wasprepared using procedures similar to those described in Example 6, butusing 6 microliters of 100 micromolar crRNA (containing the soybean PDSguide RNA sequences described above) annealed with 6 microliters of 100micromolar tracrRNA, and complexed with 20 micrograms Cas9 nuclease. TheRNP preparation was added to a tube of 1× gold microparticles in 50microliters water, mixed gently, and used at a rate of 14 microlitersRNP-coated gold per macrocarrier. Sixty microliters 2.5 molar calciumchloride and 20 microliters 0.1 molar spermidine were optionally added,with vortexing, to this preparation. (To conserve the amount of goldused, one tube of ˜1.5 mg of gold coated with 5 micrograms Cas9complexed with 2.5 micrograms crRNA-tracrRNA complex is sufficient for 9shots.) The samples were dried in Petri dishes with Drierite desiccant(W. A. Hammond DRIERITE Co., LTD, Xenia, Ohio) for 1-2 hours. The restof the bombardment procedure was similar to that described above for theDNA-coated gold microparticles.

The shoot apical meristems of 48 soybean embryonic axes were sampled 5days after bombardment by RNPs containing GmPDS g.RNA4 (SEQ ID NO:44).PCR amplification flanking the guide region was performed and sixproducts were pooled together prior to Monarch PCR purification. TheGmPDS gRNA.4 sequence contains a StyI restriction site which allows forenrichment of edited sequences; StyI restriction digest of the wild-type(unedited) sequence enriches the sample for edited sequences. After PCRpurification, the products were digested for 4 hours with StyI at 37degrees Celsius. The reactions were loaded on 2% E-gels (Invitrogen,Carlsbad, Calif.) and the uncut ˜280 base-pair product was excised andpurified using the Monarch Gel Extraction kit (New England Biolabs). Theeluted product was submitted for Sanger sequencing and analyzed forediting. From the six pools representing 48 bombarded soybean axes, onepool showed evidence of editing at the correct location on the genomepredicted to be edited by the GmPDS g.RNA4 (SEQ ID NO:44) guidesequence.

Addition bombardment experiments using GmPDS gRNA.1 (SEQ ID NO:41)delivered as DNA-coated or RNP-coated gold microparticles, or GmPDSgRNA.1 (SEQ ID NO:41) and GmPDS gRNA.2 (SEQ ID NO:42) delivered asRNP-coated gold microparticles, were evaluated for editing of theendogenous soybean PDS genes by various molecular assays, including, e.g., T7E1 assay, fragment analyzer assay, Sanger sequencing, andenrichment of edited amplicons by restriction digest and NGS ampliconsequencing.

One of skill in the art would recognize that there are alternativereagents and compositions (e. g., DNA encoding a nuclease or RNPsincluding a nuclease) including such reagents that are useful forintroducing alterations or edits into the genome (e. g., use of CRISPRnucleases other than Cas9, such as CasX, CasY, and Cpf1, zinc-fingernucleases (ZFNs), transcription activator-like effector nucleases(TAL-effector nucleases or TALENs), Argonaute proteins, or ameganuclease or engineered meganuclease) and thus similar embodiments ofthe bombardment technique described herein include use of any of thesereagents or compositions. Similarly, the bombardment technique describedherein is generally applicable to any plant part, plant tissue, or wholeplant, seed, seedling, or embryo (e. g., excised embryos, callus, leafor other plant part, meristematic tissue), and of any plant species (e.g., alfalfa (Medicago sativa), almonds (Prunus dulcis), apples (Malus xdomestica), apricots (Prunus armeniaca, P. brigantine, P. mandshurica,P. mume, P. sibirica), asparagus (Asparagus officinalis), bananas (Musaspp.), barley (Hordeum vulgare), beans (Phaseolus spp.), blueberries andcranberries (Vaccinium spp.), cacao (Theobroma cacao), canola andrapeseed or oilseed rape, (Brassica napus), carnation (Dianthuscaryophyllus), carrots (Daucus carota sativus), cassava (Manihotesculentum), cherry (Prunus avium), chickpea (Cider arietinum), chicory(Cichorium intybus), chili peppers and other capsicum peppers (Capsicumannuum, C. frutescens, C. chinense, C. pubescens, C. baccatum),chrysanthemums (Chrysanthemum spp.), coconut (Cocos nucifera), coffee(Coffea spp. including Coffea arabica and Coffea canephora), cotton(Gossypium hirsutum L.), cowpea (Vigna unguiculata), cucumber (Cucumissativus), currants and gooseberries (Ribes spp.), eggplant or aubergine(Solanum melongena), eucalyptus (Eucalyptus spp.), flax (Linumusitatissumum L.), geraniums (Pelargonium spp.), grapefruit (Citrus xparadisi), grapes (Vitus spp.) including wine grapes (Vitus vinifera),guava (Psidium guajava), irises (Iris spp.), lemon (Citrus limon),lettuce (Lactuca sativa), limes (Citrus spp.), maize (Zea mays L.),mango (Mangifera indica), mangosteen (Garcinia mangostana), melon(Cucumis melo), millets (Setaria spp, Echinochloa spp, Eleusine spp,Panicum spp., Pennisetum spp.), oats (Avena sativa), oil palm (Ellisquineensis), olive (Olea europaea), onion (Allium cepa), orange (Citrussinensis), papaya (Carica papaya), peaches and nectarines (Prunuspersica), pear (Pyrus spp.), pea (Pisa sativum), peanut (Arachishypogaea), peonies (Paeonia spp.), petunias (Petunia spp.), pineapple(Ananas comosus), plantains (Musa spp.), plum (Prunus domestica),poinsettia (Euphorbia pulcherrima), Polish canola (Brassica rapa),poplar (Populus spp.), potato (Solanum tuberosum), pumpkin (Cucurbitapepo), rice (Oryza sativa L.), roses (Rosa spp.), rubber (Heveabrasiliensis), rye (Secale cereale), safflower (Carthamus tinctorius L),sesame seed (Sesame indium), sorghum (Sorghum bicolor), soybean (Glycinemax L.), squash (Cucurbita pepo), strawberries (Fragaria spp., Fragariax ananassa), sugar beet (Beta vulgaris), sugarcanes (Saccharum spp.),sunflower (Helianthus annus), sweet potato (Ipomoea batatas), tangerine(Citrus tangerina), tea (Camellia sinensis), tobacco (Nicotiana tabacumL.), tomato (Lycopersicon esculentum), tulips (Tulipa spp.), turnip(Brassica rapa rapa), walnuts (Juglans spp. L.), watermelon (Citruluslanatus), wheat (Tritium aestivum), and yams (Discorea spp.)).Non-limiting embodiments include microparticle or nanoparticlebombardment delivery of DNA or RNP editing reagents to embryos, seeds,seedlings, meristematic tissue, or callus of maize, rice, wheat, barley,rye, millet, sorghum, soybean, cotton, brassicas (including oilseedbrassicas and sugar beet), solanaceous plants (including tomato, pepper,potato, and eggplant), strawberry, banana, plantain, citrus fruits,coffee, cacao, and sugarcanes.

Example 8

This example illustrates a method of delivering at least one effectormolecule to a plant cell wherein the plant cell is located in a plant orplant part. This example illustrates a method of delivering apolynucleotide composition including at least one crRNA or gRNA or sgRNAto a non-epidermal plant cell in a seed of a plant, resulting in editingof at least one endogenous plant gene: in this case, wheat phytoenedesaturase (PDS) genes in germline cells of wheat (Triticum aestivum)seeds. More specifically, this example illustrates a method of effectinga genetic alteration in the genome of a whole seed or part of a seed,comprising imbibition of the whole seed or part of a seed in an aqueoussolution that comprises: (a) an RNA-guided nuclease or a polynucleotidethat encodes the RNA-guided nuclease, and (b) at least one guide RNA orpolynucleotide encoding a guide RNA; wherein the at least one guide RNAis capable of directing the RNA-guided nuclease to a defined location inthe genome, thereby effecting a genetic alteration at the definedlocation in the genome; and wherein the genetic alteration is at leastone alteration selected from the group consisting of insertion of atleast one nucleotide, deletion of at least one nucleotide, orreplacement of at least one nucleotide at the defined location in thegenome. This non-limiting example demonstrates direct delivery byimbibition of effector molecules including polynucleotides encodingsingle-guide RNAs (sgRNAs) and a polynucleotide that encodes anRNA-guided nuclease, through multiple barriers (e. g., multiple celllayers, seed coat, cell walls, plasma membrane) directly into germlinecells of Triticum aestivum seeds, resulting in an alteration of thetarget nucleotide sequence, PDS. The methods described do not employ thecommon techniques of bacterially mediated transformation (e. g., byAgrobacterium sp.) or biolistics.

Common or bread wheat, Triticum aestivum, is an allohexaploid. The threewheat genomes, i. e., the wheat 4A, 4B, and 4D genomes each contain aphytoene desaturase (PDS) gene, respectively: TaPDS-4A (SEQ ID NO:45),TaPDS-4B (SEQ ID NO:46), and TaPDS-4D (SEQ ID NO:47). Three vectors weredesigned for editing the endogenous wheat PDS genes. One vector (SEQ IDNO:48, Table 6) was designed for expression of Cas9 nuclease. Twovectors (SEQ ID NO:49, Table 7 and SEQ ID NO:50, Table 8) were designedfor expression of sgRNAs; one of skill would understand that other sgRNAsequences for alternative target genes could be substituted in theplasmid.

TABLE 6 pVL40.52 Cas9 vector (SEQ ID NO: 48), 9453 base pairs DNANucleotide position in SEQ ID NO: Description Comment   1-9453 Intactplasmid SEQ ID NO: 48 378-395 M13 forward primer for sequencing 439-1557 Oryza sativa Actin 1 promoter 1558-1620 Oryza sativa Actin1,5′- Also includes untranslated leader sequence exon 1 1621-1703 Oryzasativa Actin 1 intron 1 1719-6161 Monocot codon optimized Cas9 with anintron 3258-3446 Potato IV2 intron Disrupts the Cas9 coding sequence6168-6414 Oryza sativa Actin 1,3′- untranslated sequence 6415-7168 Oryzasativa Actin 1 terminator 7228-7248 M13 reverse primer for sequencingComplement 7280-7310 Lac promoter for the E. Coli lac operon 7616-8298High copy number ColE1/pMB1/ Complement pBR322/pUC origin of replication8396-9055 CDS for bla, beta-lactamase, Complement, AmpR ampicillinselection

TABLE 7 pVL40.30 “PDS guide 2” sgRNA vector (SEQ ID NO: 49), 3493 basepairs DNA Nucleotide position in SEQ ID NO: Description Comment   1-3493Intact plasmid SEQ ID NO: 49  272-1462 Tet Tetracycline resistancemarker 1637-1655 T7 promoter for sequencing 1765-2063 Oryza sativa U6promoter 2064-2083 Oryza sativa phytoene either “PDS guide 2” fordesaturase targeting TaPDS-4A, SEQ ID NO: sequence (gRNA, not showing52) or “PDS guide 2” the PAM sequence) for TaPDS-4B or TaPDS- 4D, SEQ IDNO: 53) 2084-2159 Guide RNA scaffold sequence SEQ ID NO: 3 for S.pyogenes CRISPR/Cas9 system 2326-2945 pBB322 origin of replication

TABLE 8 pVL40.23 “PDS guide 1” sgRNA vector (SEQ ID NO: 50), 3493 basepairs DNA Nucleotide position in SEQ ID NO: Description Comment   1-3493Intact plasmid SEQ ID NO: 50  272-1462 Tet Tetracycline resistancemarker 1637-1655 T7 promoter for sequencing 1765-2063 Oryza sativa U6promoter 2064-2083 Oryza sativa phytoene “PDS guide 1”, desaturasetargeting SEQ ID NO: 51 sequence (gRNA, not showing the PAM sequence)2084-2159 Guide RNA scaffold sequence SEQ ID NO: 3 for S. pyogenesCRISPR/Cas9 system 2326-2945 pBB322 origin of replication

Glenn hard red spring wheat seed (product ID 292G, Johnny's SelectedSeed, Fairfield, Me.) were surface sterilized by wetting in 95% ethanolfor 1 minute at room temperature followed by 20 minutes in sterilizationsolution (20% bleach, 0.1% Tween-20) on a rocker at room temperature.Seed were rinsed 5 times with sterile water and air dried in a sterilelaminar flow hood, then stored in the dark in a low humidity environmentuntil use.

Twenty seed were rehydrated in 2 milliliters of sterile imbibitionsolution (15 millimolar sodium chloride, 1.5 millimolar sodium citrate,20% dimethylsulfoxide) containing 100 micrograms each of: (1) pVL40.52Cas9 vector (SEQ ID NO:48) (Table 6), (2) pVL40.23 “PDS guide 1” sgRNAvector (SEQ ID NO:50) (Table 8) including the TaPDS “PDS guide 1” sgRNAsequence (as the DNA equivalent, not showing the PAM sequence)TTTGCCATGCCAAACAAACC (“PDS guide 1” common to TaPDS-4A, TaPDS-4B, andTaPDS-4D, SEQ ID NO:51), and (3) pVL40.30 “PDS guide 2” sgRNA vector(SEQ ID NO:49) (Table 7) including one of the TaPDS “PDS guide 2” sgRNAsequences (as the DNA equivalent, not showing the PAM sequence), i. e.,TCCTGATCGGGTCAACGACG (“PDS guide 2” for TaPDS-4A, SEQ ID NO:52) orTCCTGATCGAGTCAACGACG (“PDS guide 2” for TaPDS-4B or TaPDS-4D, SEQ IDNO:53), for 42-58 hours in darkness at room temperature (22 degreesCelsius). A control treatment was treated similarly with an imbibitionsolution lacking any plasmid DNA. After imbibition, seeds were washedwith sterile water then placed in sterile petri dishes in a growthcabinet (16/8 hour light/dark cycle; 24/20 degrees Celsius) to germinatefor approximately 7 days.

The first two leaves from each germinated seedling were excised andpooled appropriately into treated or control groups. Genomic DNA (gDNA)was extracted using the CTAB procedure (Doyle, J. J. and J. L. Doyle(1987) Phytochem. Bull., 19:11-15). The gDNA template was subjected toPCR amplification using primers O-696 (CTTTTCAGTTGGAGCTTATCCCA, SEQ IDNO:54) and O-697 (CCTGCTGAAAAGAAGGTGGTCATAC, SEQ ID NO:55) at 0.5micromolar, with 100 nanograms gDNA template, 25 microliters of Phusion2× Master Mix (New England Biolabs, Ipswich, Mass.) in a 50 microliterreaction mix. The thermocycling program consisted of 98 degrees Celsiusfor 1 minute followed by 30 cycles of 98 degrees Celsius for 10 seconds,55 degrees Celsius for 10 seconds and 72 degrees Celsius for 105seconds. The final extension was 72 degrees Celsius for 10 minutes.Products were resolved by loading 20 microliters of each reaction on a1% E-gel (Invitrogen, Carlsbad, Calif.). The wild-type or non-edited(1778 base pair) band was excised and the DNA purified using the Monarchgel extraction kit (New England Biolabs). The DNA was subjected toSanger sequence analysis using the same primers used for the PCRamplification (SEQ ID NO:54 and SEQ ID NO:55).

The sequencing results showed evidence of Cas9 activity at the TaPDS“PDS guide 1” sgRNA cut site. To further refine results, PDS primers(Table 9) specific to the wheat 4A, 4B and 4D genome were used toamplify each copy in isolation for sequence analysis. The gDNA from 15plants was prepared using the CTAB method. PCR conditions were identicalto those used in the previous amplification. Products were resolved byloading 20 microliters of each reaction on a 1% E-gel (Invitrogen).

TABLE 9 Genome-specific primers for wheat phytoene desaturase SEQ ID SEQID Genome Primer 1 NO: Primer 2 NO: 4A MZ139_TaPDS_4A-F SEQ IDMZ142_TaPDS- SEQ ID NO: 56 4a,4b,4d-R NO: 57 4B MZ155-TaPDS-4B-F SEQ IDMZ142_TaPDS- SEQ ID NO: 58 4a,4b,4d-R NO: 57 4D MZ148_TaPDS_4D-F SEQ IDMZ142_TaPDS- SEQ ID NO: 59 4a,4b,4d-R NO: 57

The ˜1.8 kb DNA bands were excised and purified using the Monarch gelextraction kit (New England Biolabs) and the DNA was subjected to Sangersequence analysis. The PDS 4A band was sequenced using primerMZ139_TaPDS_4A-F (SEQ ID NO:56), the PDS 4B band was sequenced usingprimer MZ164 (NNNNNNCAGTTGGAGCTTATCCCAATGTAC, SEQ ID NO:60) and the PDS4D band was sequenced using MZ148_TaPDS_4D-F (SEQ ID NO:59). The resultsare shown in Table 10. Under these experimental conditions, the majorityof Cas9 editing activity (genomic alterations) was detected at the4B-PDS gene; no Cas9 editing activity (genomic alterations) was detectedat the 4A-PDS gene and in one line (#9) at the 4D-PDS gene.

TABLE 10 Plant 4A-PDS 4B-PDS 4D-PDS Control wt wt wt 1 wt Edited atguide#1 wt 2 wt Edited at guide#1 wt 3 wt wt wt 4 wt wt wt 5 wt wt wt 6wt wt wt 7 wt wt wt 8 wt wt wt 9 wt Edited at guide#1 Edited at guide#110 wt Edited at guide#1 wt 11 wt PCR failed wt 12 wt Edited at guide#1wt 13 wt Not analyzed* wt 14 wt Not analyzed* wt 15 wt Not analyzed* wtwt = wild-type sequence (unedited) *not enough gDNA left for analysis

Wheat seeds that have been subjected to this imbibition/editingtreatment can also be grown out for observation of a visible bleachedphenotype due to modification of the endogenous PDS gene(s) results in aplant having an observable bleached phenotype. Plants that survive toreproductive maturity are allowed to set seed, and progeny seed aresubjected to molecular analysis for the presence of heritablealterations to one or more of the endogenous PDS genes(s).

One of skill in the art would recognize that there are alternativereagents and compositions (e. g., DNA encoding a nuclease or RNPsincluding a nuclease) including such reagents that are useful forintroducing alterations or edits into the genome (e. g., use of CRISPRnucleases other than Cas9, such as CasX, CasY, and Cpf1, zinc-fingernucleases (ZFNs), transcription activator-like effector nucleases(TAL-effector nucleases or TALENs), Argonaute proteins, or ameganuclease or engineered meganuclease) and thus similar embodiments ofthe imbibition technique described herein include use of any of thesereagents or compositions. Similarly, the imbibition technique describedherein is generally applicable to any plant part, plant tissue, or wholeplant, seed, seedling, or embryo (e. g., whole seed or part of a seed,excised embryos, callus, leaf or other plant part, meristematic tissue),and of any plant species (e. g., alfalfa (Medicago sativa), almonds(Prunus dulcis), apples (Malus x domestica), apricots (Prunus armeniaca,P. brigantine, P. mandshurica, P. mume, P. sibirica), asparagus(Asparagus officinalis), bananas (Musa spp.), barley (Hordeum vulgare),beans (Phaseolus spp.), blueberries and cranberries (Vaccinium spp.),cacao (Theobroma cacao), canola and rapeseed or oilseed rape, (Brassicanapus), carnation (Dianthus caryophyllus), carrots (Daucus carotasativus), cassava (Manihot esculentum), cherry (Prunus avium), chickpea(Cider arietinum), chicory (Cichorium intybus), chili peppers and othercapsicum peppers (Capsicum annuum, C. frutescens, C. chinense, C.pubescens, C. baccatum), chrysanthemums (Chrysanthemum spp.), coconut(Cocos nucifera), coffee (Coffea spp. including Coffea arabica andCoffea canephora), cotton (Gossypium hirsutum L.), cowpea (Vignaunguiculata), cucumber (Cucumis sativus), currants and gooseberries(Ribes spp.), eggplant or aubergine (Solanum melongena), eucalyptus(Eucalyptus spp.), flax (Linum usitatissumum L.), geraniums (Pelargoniumspp.), grapefruit (Citrus x paradisi), grapes (Vitus spp.) includingwine grapes (Vitus vinifera), guava (Psidium guajava), irises (Irisspp.), lemon (Citrus limon), lettuce (Lactuca sativa), limes (Citrusspp.), maize (Zea mays L.), mango (Mangifera indica), mangosteen(Garcinia mangostana), melon (Cucumis melo), millets (Setaria spp,Echinochloa spp, Eleusine spp, Panicum spp., Pennisetum spp.), oats(Avena sativa), oil palm (Ellis quineensis), olive (Olea europaea),onion (Allium cepa), orange (Citrus sinensis), papaya (Carica papaya),peaches and nectarines (Prunus persica), pear (Pyrus spp.), pea (Pisasativum), peanut (Arachis hypogaea), peonies (Paeonia spp.), petunias(Petunia spp.), pineapple (Ananas comosus), plantains (Musa spp.), plum(Prunus domestica), poinsettia (Euphorbia pulcherrima), Polish canola(Brassica rapa), poplar (Populus spp.), potato (Solanum tuberosum),pumpkin (Cucurbita pepo), rice (Oryza sativa L.), roses (Rosa spp.),rubber (Hevea brasiliensis), rye (Secale cereale), safflower (Carthamustinctorius L), sesame seed (Sesame indium), sorghum (Sorghum bicolor),soybean (Glycine max L.), squash (Cucurbita pepo), strawberries(Fragaria spp., Fragaria x ananassa), sugar beet (Beta vulgaris),sugarcanes (Saccharum spp.), sunflower (Helianthus annus), sweet potato(Ipomoea batatas), tangerine (Citrus tangerina), tea (Camelliasinensis), tobacco (Nicotiana tabacum L.), tomato (Lycopersiconesculentum), tulips (Tulipa spp.), turnip (Brassica rapa rapa), walnuts(Juglans spp. L.), watermelon (Citrulus lanatus), wheat (Tritiumaestivum), and yams (Discorea spp.)). Non-limiting embodiments includeimbibition delivery of DNA or RNP editing reagents to whole seed or partof a seed, embryos, callus, pollen, anthers, stamens, leaf or otherplant part, and meristematic tissue of maize, rice, wheat, barley, rye,millet, sorghum, soybean, cotton, brassicas (including oilseed brassicasand sugar beet), solanaceous plants (including tomato, pepper, potato,and eggplant), strawberry, banana, plantain, citrus fruits, coffee,cacao, and sugarcanes.

All cited patents and patent publications referred to in thisapplication are incorporated herein by reference in their entirety. Allof the materials and methods disclosed and claimed herein can be madeand used without undue experimentation as instructed by the abovedisclosure and illustrated by the examples. Although the materials andmethods of this invention have been described in terms of embodimentsand illustrative examples, it will be apparent to those of skill in theart that substitutions and variations can be applied to the materialsand methods described herein without departing from the concept, spirit,and scope of the invention. For instance, while the particular examplesprovided illustrate the methods and embodiments described herein using aspecific plant, the principles in these examples are applicable to anyplant of interest; similarly, while the particular examples providedillustrate the methods and embodiments described herein using aparticular sequence-specific nuclease such as Cas9, one of skill in theart would recognize that alternative sequence-specific nucleases (e. g.,CRISPR nucleases other than Cas9, such as CasX, CasY, and Cpf1,zinc-finger nucleases, transcription activator-like effector nucleases,Argonaute proteins, and meganucleases) are useful in variousembodiments. All such similar substitutes and modifications apparent tothose skilled in the art are deemed to be within the spirit, scope, andconcept of the invention as encompassed by the embodiments of theinventions recited herein and the specification and appended claims.

What is claimed:
 1. A method of effecting a genetic alteration in thegenome of a whole seed or part of a seed, comprising imbibition of thewhole seed or part of a seed in a polynucleotide composition thatcomprises: (a) an RNA-guided nuclease or a polynucleotide that encodesthe RNA-guided nuclease, and (b) at least one guide RNA orpolynucleotide encoding a guide RNA; wherein the at least one guide RNAis capable of directing the RNA-guided nuclease to a defined location inthe genome, thereby effecting a genetic alteration at the definedlocation in the genome; wherein the genetic alteration is at least onealteration selected from the group consisting of insertion of at leastone nucleotide, deletion of at least one nucleotide, or replacement ofat least one nucleotide at the defined location in the genome.
 2. Awhole seed or part of a seed comprising a genetic alteration in itsgenome, provided by the method of claim 1, or a plant grown orregenerated from the whole seed or part of a seed, wherein the plantcomprises cells comprising the genetic alteration in their genome andoptionally is grown directly from the whole seed or part of a seedwithout a callus stage.
 3. A method of effecting a genetic alteration inthe genome of embryonic plant tissue, comprising bombardment of theembryonic plant tissue with a polynucleotide composition comprising aparticle complexed with a ribonucleoprotein (RNP) comprising anRNA-guided nuclease and at least one guide RNA (gRNA) having anucleotide sequence designed to alter a target nucleotide sequence inthe genome, thereby effecting the genetic alteration.
 4. A method ofdelivering a guide RNA (gRNA) to a non-epidermal plant cell, wherein thenon-epidermal plant cell is in a plant or part of a plant, wherein thegRNA has a nucleotide sequence designed to alter a target nucleotidesequence in the non-epidermal plant cell, and wherein the gRNA isprovided as a polynucleotide composition comprising: (i) a CRISPR RNA(crRNA) that includes the gRNA, or a polynucleotide that encodes acrRNA, or a polynucleotide that is processed into a crRNA; or (ii) asingle guide RNA (sgRNA) that includes the gRNA, or a polynucleotidethat encodes an sgRNA, or a polynucleotide that is processed into ansgRNA; wherein the delivery of the polynucleotide composition comprisesat least one treatment selected from the group consisting of:microinjection and mechanical cell wall breakage; and wherein thenon-epidermal plant cell, or the plant or plant part in which thenon-epidermal plant cell is located, is subjected to heating or heatstress; whereby the gRNA is delivered to the non-epidermal plant celland the target nucleotide sequence in the non-epidermal plant cell isaltered.
 5. The method of claim 4, wherein the plant or part of a plantis selected from the group consisting of a plant tissue, a whole plant,an intact nodal bud, a shoot apex or shoot apical meristem, a root apexor root apical meristem, lateral meristem, intercalary meristem, aseedling, a whole seed, a halved seed or other seed fragment, an embryo,and callus.
 6. The method of claim 4, wherein: (a) the polynucleotidecomposition optionally comprises an RNA-guided nuclease, or apolynucleotide that encodes the RNA-guided nuclease; or (b) the methodfurther includes the step of providing to the non-epidermal plant cellan RNA-guided nuclease or a polynucleotide that encodes the RNA-guidednuclease; or (c) the non-epidermal plant cell comprises an RNA-guidednuclease or a polynucleotide that encodes the RNA-guided nuclease. 7.The method of claim 1, 3, or 4, wherein (a) the polynucleotidecomposition further comprises a chemical agent or a physical agent or acombination of both chemical and physical agents, or (b) the methodfurther comprises the step of treating the plant cell with a chemicalagent or a physical agent or a combination of both chemical and physicalagents; wherein the chemical agent is at least one selected from thegroup consisting of solvents, fluorocarbons, glycols or polyols,surfactants; primary, secondary, or tertiary amines and quaternaryammonium salts; saponins; organosilicone surfactants; lipids,lipoproteins, lipopolysaccharides; acids, bases, caustic agents;peptides, proteins, or enzymes; cell-penetrating peptides; RNaseinhibitors; cationic branched or linear polymers; dendrimers;counter-ions, amines or polyamines, osmolytes, buffers, and salts;polynucleotides; transfection agents; antibiotics; non-specific DNAdouble-strand-break-inducing agents; antioxidants; and chelating agents;and wherein the physical agent is at least one selected from the groupconsisting of particles or nanoparticles, magnetic particles ornanoparticles, abrasive or scarifying agents, needles or microneedles,matrices, and grids.
 8. The method of claim 4, wherein the crRNA, thepolynucleotide that encodes a crRNA, the polynucleotide that isprocessed into a crRNA, the sgRNA, the polynucleotide that encodes ansgRNA, or the polynucleotide that is processed into an sgRNA furthercomprises one or more additional nucleotide sequences selected from thegroup consisting of an aptamer or riboswitch sequence, a nucleotidesequence that provides secondary structure, a nucleotide sequence thatprovides a sequence-specific site for an enzyme, T-DNA sequence, a DNAnuclear-targeting sequence, a regulatory sequence, and atranscript-stabilizing sequence.
 9. The method of claim 4, wherein thecrRNA, the polynucleotide that encodes a crRNA, the polynucleotide thatis processed into a crRNA, the sgRNA, the polynucleotide that encodes ansgRNA, or the polynucleotide that is processed into an sgRNA comprises:(a) double-stranded RNA, (b) single-stranded RNA; (c) chemicallymodified RNA; (d) a combination of (a)-(c).
 10. The method of claim 6,wherein the RNA-guided nuclease or polynucleotide that encodes theRNA-guided nuclease is provided: (a) as a ribonucleoprotein complexcomprising the crRNA and the RNA-guided nuclease; (b) as a complexcomprising the RNA-guided nuclease or polynucleotide that encodes theRNA-guided nuclease and at least one peptide selected from the groupconsisting of a cell-penetrating peptide, viral movement protein, ortransfecting peptide; (c) as a fusion protein comprising the RNA-guidednuclease and at least one peptide selected from the group consisting ofa cell-penetrating peptide, viral movement protein, or transfectingpeptide; (d) on a carrier molecule or a particulate; (e) in a liposome,micelle, protoplast or protoplast fragment; (f) using a combination ofany of (a)-(e).
 11. The method of claim 6, wherein the RNA-guidednuclease is provided: (a) by contacting the non-epidermal plant cellwith the RNA-guided nuclease or polynucleotide that encodes theRNA-guided nuclease; (b) by transporting the RNA-guided nuclease orpolynucleotide that encodes the RNA-guided nuclease into thenon-epidermal plant cell using a chemical, enzymatic, or physical agent;(c) by bacterially mediated transfection with a polynucleotide encodingthe RNA-guided nuclease; or (d) by transcription of a polynucleotidethat encodes the RNA-guided nuclease.
 12. The method of claim 4, whereinthe polynucleotide composition comprises a liquid, a solution, asuspension, an emulsion, a reverse emulsion, a colloid, a dispersion, agel, liposomes, micelles, an injectable material, an aerosol, a solid, apowder, a particulate, a nanoparticle, or a combination thereof.
 13. Anon-epidermal plant cell comprising an altered target nucleotidesequence, provided by the method of claim 4, or a plant grown orregenerated from the non-epidermal plant cell comprising an alteredtarget nucleotide sequence, wherein the plant comprises cells having thealtered target nucleotide sequence, or seed or plant parts of the plant.14. The method of claim 4, wherein the non-epidermal plant cell ishaploid, wherein the method further comprises the step of chromosomedoubling in the non-epidermal plant cell comprising the altered targetnucleotide sequence to produce a doubled haploid cell that is homozygousfor the altered target nucleotide sequence.
 15. The doubled haploid cellthat is homozygous for the altered target nucleotide sequence, providedby the method of
 14. 16. The method of claim 14, further comprisingregeneration of a doubled haploid plant from the doubled haploid cell,wherein the regenerated doubled haploid plant comprises cells that arehomozygous for the altered target nucleotide sequence.
 17. Theregenerated doubled haploid plant provided by the method of claim 16, orseed or plant parts of the regenerated doubled haploid plant, or ahybrid plant having at least one parent plant that is the regenerateddoubled haploid plant.
 18. The method of any of claim 1, 3, or 6,wherein the RNA-guided nuclease is selected from the group consisting ofan RNA-guided DNA endonuclease, a type II Cas nuclease, a Cas9, a type VCas nuclease, a Cpf1, a CasY, a CasX, a C2c1, a C2c3, an engineerednuclease, and a codon-optimized nuclease.
 19. The method of claim 1, 3,or 4, wherein the genetic alteration is heritable to succeedinggenerations.
 20. A plant grown or regenerated from the embryonic planttissue having the genetic alteration in its genome provided by themethod of claim 3, wherein the plant comprises cells comprising thegenetic alteration in their genome and optionally is grown directly fromthe whole seed or part of a seed without a callus stage.